Saccharomyces Cerevisiae RNA-seq
#Set working directory
setwd("C:/Users/benfu/Documents/BIOL3008")#Install BiocManager
install.packages("BiocManager")#Checking for updates
BiocManager::install()'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.3 (2023-03-15 ucrt)
Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.2.3/library
packages:
class, KernSmooth, lattice, MASS, Matrix, nnet, survival
Old packages: 'DelayedArray', 'jsonlite', 'matrixStats'Update all/some/none? [a/s/n]: install.packages("BiocManager")Update all/some/none? [a/s/n]: aWarning: downloaded length 0 != reported length 594Warning: cannot open URL 'http://archive.bioconductor.org.s3-website-us-east-1.amazonaws.com/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 593Warning: cannot open URL 'http://archive.bioconductor.org.s3-website-us-east-1.amazonaws.com/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 594Warning: cannot open URL 'http://archive.bioconductor.org.s3-website-us-east-1.amazonaws.com/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 593Warning: cannot open URL 'http://archive.bioconductor.org.s3-website-us-east-1.amazonaws.com/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 588Warning: cannot open URL 'http://archive.bioconductor.org.s3-website-us-east-1.amazonaws.com/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 587Warning: cannot open URL 'http://archive.bioconductor.org.s3-website-us-east-1.amazonaws.com/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'
There are binary versions available but the source versions are later:
Binaries will be installedtrying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/DelayedArray_0.23.2.zip'
Content type 'application/zip' length 2449113 bytes (2.3 MB)
downloaded 2.3 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/jsonlite_1.8.4.zip'
Content type 'application/zip' length 1105031 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/matrixStats_1.0.0.zip'
Content type 'application/zip' length 528199 bytes (515 KB)
downloaded 515 KBpackage 'DelayedArray' successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package 'DelayedArray'Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\DelayedArray\libs\x64\DelayedArray.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\DelayedArray\libs\x64\DelayedArray.dll: Permission deniedWarning: restored 'DelayedArray'package 'jsonlite' successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package 'jsonlite'Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\jsonlite\libs\x64\jsonlite.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\jsonlite\libs\x64\jsonlite.dll: Permission deniedWarning: restored 'jsonlite'package 'matrixStats' successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package 'matrixStats'Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\matrixStats\libs\x64\matrixStats.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\matrixStats\libs\x64\matrixStats.dll: Permission deniedWarning: restored 'matrixStats'
The downloaded binary packages are in
C:\Users\benfu\AppData\Local\Temp\Rtmp4GqjmM\downloaded_packages#Installing Rsubread
BiocManager::install("Rsubread")'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.3 (2023-03-15 ucrt)
Warning: package(s) not installed when version(s) same as or greater than current; use
`force = TRUE` to re-install: 'Rsubread'Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.2.3/library
packages:
class, KernSmooth, lattice, MASS, Matrix, nnet, survival
Old packages: 'DelayedArray', 'jsonlite', 'matrixStats'Update all/some/none? [a/s/n]: aWarning: downloaded length 0 != reported length 594Warning: cannot open URL 'http://archive.bioconductor.org.s3-website-us-east-1.amazonaws.com/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 593Warning: cannot open URL 'http://archive.bioconductor.org.s3-website-us-east-1.amazonaws.com/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 594Warning: cannot open URL 'http://archive.bioconductor.org.s3-website-us-east-1.amazonaws.com/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 593Warning: cannot open URL 'http://archive.bioconductor.org.s3-website-us-east-1.amazonaws.com/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 588Warning: cannot open URL 'http://archive.bioconductor.org.s3-website-us-east-1.amazonaws.com/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 587Warning: cannot open URL 'http://archive.bioconductor.org.s3-website-us-east-1.amazonaws.com/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'
There are binary versions available but the source versions are later:
Binaries will be installedtrying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/DelayedArray_0.23.2.zip'
Content type 'application/zip' length 2449113 bytes (2.3 MB)
downloaded 2.3 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/jsonlite_1.8.4.zip'
Content type 'application/zip' length 1105031 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/matrixStats_1.0.0.zip'
Content type 'application/zip' length 528199 bytes (515 KB)
downloaded 515 KBpackage 'DelayedArray' successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package 'DelayedArray'Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\DelayedArray\libs\x64\DelayedArray.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\DelayedArray\libs\x64\DelayedArray.dll: Permission deniedWarning: restored 'DelayedArray'package 'jsonlite' successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package 'jsonlite'Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\jsonlite\libs\x64\jsonlite.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\jsonlite\libs\x64\jsonlite.dll: Permission deniedWarning: restored 'jsonlite'package 'matrixStats' successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package 'matrixStats'Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\matrixStats\libs\x64\matrixStats.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\matrixStats\libs\x64\matrixStats.dll: Permission deniedWarning: restored 'matrixStats'
The downloaded binary packages are in
C:\Users\benfu\AppData\Local\Temp\Rtmp4GqjmM\downloaded_packages#Loading Rsubread
library(Rsubread)#Indexing reference genome
buildindex(basename = "Yeast", reference = "Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz")
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.12.3
//================================= setting ==================================\\
|| ||
|| Index name : Yeast ||
|| Index space : base space ||
|| Index split : no-split ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
|| Free / total memory : 0.9GB / 7.6GB ||
|| ||
|| Input files : 1 file in total ||
|| o Saccharomyces_cerevisiae.R64-1-1.dna.top ... ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Check the integrity of provided reference sequences ... ||
|| No format issues were found ||
|| Scan uninformative subreads in reference sequences ... ||
|| 11 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Estimate the index size... ||
|| 8%, 0 mins elapsed, rate=2482.4k bps/s ||
|| 16%, 0 mins elapsed, rate=2959.7k bps/s ||
|| 24%, 0 mins elapsed, rate=2984.6k bps/s ||
|| 33%, 0 mins elapsed, rate=2953.6k bps/s ||
|| 41%, 0 mins elapsed, rate=2975.4k bps/s ||
|| 49%, 0 mins elapsed, rate=2897.5k bps/s ||
|| 58%, 0 mins elapsed, rate=2870.8k bps/s ||
|| 66%, 0 mins elapsed, rate=2944.9k bps/s ||
|| 74%, 0 mins elapsed, rate=2971.9k bps/s ||
|| 83%, 0 mins elapsed, rate=2982.6k bps/s ||
|| 91%, 0 mins elapsed, rate=3021.9k bps/s ||
|| ||
|| WARNING: available memory is lower than 3.0 GB. ||
|| The program may run very slow. ||
|| Build a gapped index and/or split index into blocks to reduce memory use. ||
|| ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=474.0k bps/s ||
|| 16%, 0 mins elapsed, rate=759.5k bps/s ||
|| 24%, 0 mins elapsed, rate=930.9k bps/s ||
|| 33%, 0 mins elapsed, rate=1079.9k bps/s ||
|| 41%, 0 mins elapsed, rate=1148.6k bps/s ||
|| 49%, 0 mins elapsed, rate=1220.1k bps/s ||
|| 58%, 0 mins elapsed, rate=1302.5k bps/s ||
|| 66%, 0 mins elapsed, rate=1372.0k bps/s ||
|| 74%, 0 mins elapsed, rate=1442.1k bps/s ||
|| 83%, 0 mins elapsed, rate=1485.8k bps/s ||
|| 91%, 0 mins elapsed, rate=1511.2k bps/s ||
|| Save current index block... ||
|| [ 0.0% finished ] ||
|| [ 10.0% finished ] ||
|| [ 20.0% finished ] ||
|| [ 30.0% finished ] ||
|| [ 40.0% finished ] ||
|| [ 50.0% finished ] ||
|| [ 60.0% finished ] ||
|| [ 70.0% finished ] ||
|| [ 80.0% finished ] ||
|| [ 90.0% finished ] ||
|| [ 100.0% finished ] ||
|| ||
|| Total running time: 0.6 minutes. ||
|| Index C:\Users\benfu\Documents\BIOL3008\Yeast was successfully built. ||
|| ||
\\============================================================================//##Mapping RNAseq reads to indexed reference genome individually as this computers disc space is limited. Unable to have all SRR*.fastq files in the directory at the same time.
#SRR20632986
align(index = "Yeast", readfile1 = "trimmed_SRR20632986_1.fastq", readfile2 = "trimmed_SRR20632986_2.fastq", type = "rna", input_format = "FASTQ", output_format = "BAM", output_file = "SRR20632986.bam", useAnnotation = TRUE, annot.ext = "Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz", isGTF = TRUE, GTF.featureType = "exon", GTF.attrType = "exon_id")
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.12.3
//================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : trimmed_SRR20632986_1.fastq ||
|| Input file 2 : trimmed_SRR20632986_2.fastq ||
|| Output file : SRR20632986.bam (BAM) ||
|| Index name : Yeast ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : yes ||
|| Max alignments per multi-mapping read : 1 ||
|| Annotations : Saccharomyces_cerevisiae.R64-1 ... ||
|| ||
\\============================================================================//
//================ Running (06-May-2023 16:00:21, pid=15132) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [2,37] ||
|| Create the output BAM file. ||
|| Check the index. ||
|| Init the voting space. ||
|| Load the annotation file. ||
|| 7507 annotation records were loaded. ||
|| Global environment is initialised. ||
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
|| 0% completed, 0.6 mins elapsed, rate=12.6k fragments per second ||
|| 6% completed, 1.6 mins elapsed, rate=15.7k fragments per second ||
|| 13% completed, 2.6 mins elapsed, rate=15.7k fragments per second ||
|| Estimated fragment length : 205 bp ||
|| 17% completed, 3.7 mins elapsed, rate=11.2k fragments per second ||
|| 18% completed, 4.0 mins elapsed, rate=10.6k fragments per second ||
|| 18% completed, 4.4 mins elapsed, rate=10.1k fragments per second ||
|| 19% completed, 4.8 mins elapsed, rate=9.7k fragments per second ||
|| 20% completed, 5.2 mins elapsed, rate=9.4k fragments per second ||
|| 21% completed, 5.5 mins elapsed, rate=9.1k fragments per second ||
|| 22% completed, 5.9 mins elapsed, rate=8.9k fragments per second ||
|| 23% completed, 6.3 mins elapsed, rate=8.6k fragments per second ||
|| 23% completed, 6.7 mins elapsed, rate=8.4k fragments per second ||
|| Start read mapping in chunk. ||
|| 24% completed, 7.4 mins elapsed, rate=8.5k fragments per second ||
|| 31% completed, 8.7 mins elapsed, rate=9.2k fragments per second ||
|| 38% completed, 9.7 mins elapsed, rate=9.9k fragments per second ||
|| 42% completed, 11 mins elapsed, rate=9.0k fragments per second ||
|| 42% completed, 11 mins elapsed, rate=8.8k fragments per second ||
|| 43% completed, 11 mins elapsed, rate=8.6k fragments per second ||
|| 44% completed, 12 mins elapsed, rate=8.4k fragments per second ||
|| 45% completed, 12 mins elapsed, rate=8.3k fragments per second ||
|| 46% completed, 13 mins elapsed, rate=8.1k fragments per second ||
|| 47% completed, 13 mins elapsed, rate=8.0k fragments per second ||
|| 47% completed, 14 mins elapsed, rate=7.9k fragments per second ||
|| 48% completed, 14 mins elapsed, rate=7.8k fragments per second ||
|| Start read mapping in chunk. ||
|| 49% completed, 15 mins elapsed, rate=7.7k fragments per second ||
|| 56% completed, 16 mins elapsed, rate=8.1k fragments per second ||
|| 62% completed, 17 mins elapsed, rate=8.6k fragments per second ||
|| 66% completed, 18 mins elapsed, rate=8.3k fragments per second ||
|| 67% completed, 19 mins elapsed, rate=8.1k fragments per second ||
|| 68% completed, 20 mins elapsed, rate=8.0k fragments per second ||
|| 69% completed, 20 mins elapsed, rate=7.9k fragments per second ||
|| 70% completed, 21 mins elapsed, rate=7.8k fragments per second ||
|| 71% completed, 21 mins elapsed, rate=7.7k fragments per second ||
|| 71% completed, 22 mins elapsed, rate=7.7k fragments per second ||
|| 72% completed, 22 mins elapsed, rate=7.6k fragments per second ||
|| 73% completed, 23 mins elapsed, rate=7.5k fragments per second ||
|| Start read mapping in chunk. ||
|| 74% completed, 23 mins elapsed, rate=7.6k fragments per second ||
|| 81% completed, 24 mins elapsed, rate=7.9k fragments per second ||
|| 87% completed, 25 mins elapsed, rate=8.2k fragments per second ||
|| 91% completed, 26 mins elapsed, rate=8.0k fragments per second ||
|| 92% completed, 27 mins elapsed, rate=7.9k fragments per second ||
|| 93% completed, 28 mins elapsed, rate=7.8k fragments per second ||
|| 94% completed, 28 mins elapsed, rate=7.7k fragments per second ||
|| 95% completed, 29 mins elapsed, rate=7.7k fragments per second ||
|| 95% completed, 29 mins elapsed, rate=7.6k fragments per second ||
|| 96% completed, 30 mins elapsed, rate=7.5k fragments per second ||
|| 97% completed, 30 mins elapsed, rate=7.4k fragments per second ||
|| 98% completed, 31 mins elapsed, rate=7.4k fragments per second ||
|| Start read mapping in chunk. ||
|| 99% completed, 31 mins elapsed, rate=7.4k fragments per second ||
|| 99% completed, 32 mins elapsed, rate=7.3k fragments per second ||
|| 99% completed, 32 mins elapsed, rate=7.3k fragments per second ||
|| 99% completed, 32 mins elapsed, rate=7.3k fragments per second ||
|| 99% completed, 32 mins elapsed, rate=7.3k fragments per second ||
|| 99% completed, 32 mins elapsed, rate=7.3k fragments per second ||
|| 99% completed, 32 mins elapsed, rate=7.3k fragments per second ||
|| 99% completed, 32 mins elapsed, rate=7.3k fragments per second ||
|| 99% completed, 32 mins elapsed, rate=7.3k fragments per second ||
|| 99% completed, 32 mins elapsed, rate=7.3k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total fragments : 14070993 ||
|| Mapped : 13904003 (98.8%) ||
|| Uniquely mapped : 13258179 ||
|| Multi-mapping : 645824 ||
|| ||
|| Unmapped : 166990 ||
|| ||
|| Properly paired : 13087791 ||
|| Not properly paired : 816212 ||
|| Singleton : 602857 ||
|| Chimeric : 150434 ||
|| Unexpected strandness : 8783 ||
|| Unexpected fragment length : 41127 ||
|| Unexpected read order : 13011 ||
|| ||
|| Indels : 59004 ||
|| ||
|| Running time : 32.2 minutes ||
|| ||
\\============================================================================//#SRR20632987
align(index = "Yeast", readfile1 = "trimmed_SRR20632987_1.fastq", readfile2 = "trimmed_SRR20632987_2.fastq", type = "rna", input_format = "FASTQ", output_format = "BAM", output_file = "SRR20632987.bam", useAnnotation = TRUE, annot.ext = "Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz", isGTF = TRUE, GTF.featureType = "exon", GTF.attrType = "exon_id")
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.12.3
//================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : trimmed_SRR20632987_1.fastq ||
|| Input file 2 : trimmed_SRR20632987_2.fastq ||
|| Output file : SRR20632987.bam (BAM) ||
|| Index name : Yeast ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : yes ||
|| Max alignments per multi-mapping read : 1 ||
|| Annotations : Saccharomyces_cerevisiae.R64-1 ... ||
|| ||
\\============================================================================//
//================= Running (08-May-2023 22:13:25, pid=5328) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [2,37] ||
|| Create the output BAM file. ||
|| Check the index. ||
|| Init the voting space. ||
|| Load the annotation file. ||
|| 7507 annotation records were loaded. ||
|| Global environment is initialised. ||
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
|| 0% completed, 0.6 mins elapsed, rate=14.9k fragments per second ||
|| 6% completed, 1.3 mins elapsed, rate=16.2k fragments per second ||
|| 13% completed, 2.0 mins elapsed, rate=16.2k fragments per second ||
|| 20% completed, 2.6 mins elapsed, rate=16.9k fragments per second ||
|| Estimated fragment length : 203 bp ||
|| 23% completed, 3.4 mins elapsed, rate=12.1k fragments per second ||
|| 24% completed, 3.7 mins elapsed, rate=11.5k fragments per second ||
|| 25% completed, 4.1 mins elapsed, rate=11.0k fragments per second ||
|| 27% completed, 4.4 mins elapsed, rate=10.6k fragments per second ||
|| 28% completed, 4.7 mins elapsed, rate=10.3k fragments per second ||
|| 29% completed, 5.1 mins elapsed, rate=9.9k fragments per second ||
|| 30% completed, 5.5 mins elapsed, rate=9.6k fragments per second ||
|| 31% completed, 5.9 mins elapsed, rate=9.3k fragments per second ||
|| 32% completed, 6.3 mins elapsed, rate=9.0k fragments per second ||
|| Start read mapping in chunk. ||
|| 33% completed, 6.9 mins elapsed, rate=9.3k fragments per second ||
|| 40% completed, 7.7 mins elapsed, rate=9.8k fragments per second ||
|| 47% completed, 8.4 mins elapsed, rate=10.3k fragments per second ||
|| 53% completed, 9.1 mins elapsed, rate=10.8k fragments per second ||
|| 57% completed, 10 mins elapsed, rate=9.8k fragments per second ||
|| 58% completed, 10 mins elapsed, rate=9.5k fragments per second ||
|| 59% completed, 11 mins elapsed, rate=9.3k fragments per second ||
|| 60% completed, 11 mins elapsed, rate=9.1k fragments per second ||
|| 62% completed, 12 mins elapsed, rate=8.9k fragments per second ||
|| 63% completed, 12 mins elapsed, rate=8.7k fragments per second ||
|| 64% completed, 12 mins elapsed, rate=8.5k fragments per second ||
|| 65% completed, 13 mins elapsed, rate=8.4k fragments per second ||
|| 66% completed, 13 mins elapsed, rate=8.2k fragments per second ||
|| Start read mapping in chunk. ||
|| 67% completed, 14 mins elapsed, rate=8.3k fragments per second ||
|| 74% completed, 15 mins elapsed, rate=8.6k fragments per second ||
|| 81% completed, 16 mins elapsed, rate=9.0k fragments per second ||
|| 87% completed, 16 mins elapsed, rate=9.3k fragments per second ||
|| 90% completed, 17 mins elapsed, rate=8.8k fragments per second ||
|| 91% completed, 18 mins elapsed, rate=8.6k fragments per second ||
|| 92% completed, 18 mins elapsed, rate=8.5k fragments per second ||
|| 93% completed, 19 mins elapsed, rate=8.4k fragments per second ||
|| 94% completed, 19 mins elapsed, rate=8.3k fragments per second ||
|| 95% completed, 20 mins elapsed, rate=8.2k fragments per second ||
|| 96% completed, 20 mins elapsed, rate=8.1k fragments per second ||
|| 97% completed, 21 mins elapsed, rate=8.0k fragments per second ||
|| 98% completed, 21 mins elapsed, rate=7.9k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total fragments : 10321097 ||
|| Mapped : 10193490 (98.8%) ||
|| Uniquely mapped : 9773149 ||
|| Multi-mapping : 420341 ||
|| ||
|| Unmapped : 127607 ||
|| ||
|| Properly paired : 9647133 ||
|| Not properly paired : 546357 ||
|| Singleton : 418660 ||
|| Chimeric : 88501 ||
|| Unexpected strandness : 4961 ||
|| Unexpected fragment length : 25692 ||
|| Unexpected read order : 8543 ||
|| ||
|| Indels : 47445 ||
|| ||
|| Running time : 22.1 minutes ||
|| ||
\\============================================================================//#SRR20632988
align(index = "Yeast", readfile1 = "trimmed_SRR20632988_1.fastq", readfile2 = "trimmed_SRR20632988_2.fastq", type = "rna", input_format = "FASTQ", output_format = "BAM", output_file = "SRR20632988.bam", useAnnotation = TRUE, annot.ext = "Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz", isGTF = TRUE, GTF.featureType = "exon", GTF.attrType = "exon_id")
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.12.3
//================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : trimmed_SRR20632988_1.fastq ||
|| Input file 2 : trimmed_SRR20632988_2.fastq ||
|| Output file : SRR20632988.bam (BAM) ||
|| Index name : Yeast ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : yes ||
|| Max alignments per multi-mapping read : 1 ||
|| Annotations : Saccharomyces_cerevisiae.R64-1 ... ||
|| ||
\\============================================================================//
//================= Running (08-May-2023 22:48:59, pid=5328) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [2,37] ||
|| Create the output BAM file. ||
|| Check the index. ||
|| Init the voting space. ||
|| Load the annotation file. ||
|| 7507 annotation records were loaded. ||
|| Global environment is initialised. ||
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
|| 0% completed, 0.6 mins elapsed, rate=8.7k fragments per second ||
|| 6% completed, 1.4 mins elapsed, rate=14.5k fragments per second ||
|| 13% completed, 2.2 mins elapsed, rate=14.7k fragments per second ||
|| 20% completed, 2.9 mins elapsed, rate=15.0k fragments per second ||
|| Estimated fragment length : 209 bp ||
|| 23% completed, 3.9 mins elapsed, rate=10.4k fragments per second ||
|| 24% completed, 4.4 mins elapsed, rate=9.8k fragments per second ||
|| 25% completed, 4.7 mins elapsed, rate=9.4k fragments per second ||
|| 26% completed, 5.2 mins elapsed, rate=9.0k fragments per second ||
|| 27% completed, 5.6 mins elapsed, rate=8.6k fragments per second ||
|| 28% completed, 6.1 mins elapsed, rate=8.3k fragments per second ||
|| 29% completed, 6.5 mins elapsed, rate=8.1k fragments per second ||
|| 30% completed, 6.8 mins elapsed, rate=8.0k fragments per second ||
|| 31% completed, 7.3 mins elapsed, rate=7.7k fragments per second ||
|| Start read mapping in chunk. ||
|| 33% completed, 8.2 mins elapsed, rate=7.6k fragments per second ||
|| 39% completed, 9.5 mins elapsed, rate=7.9k fragments per second ||
|| 46% completed, 10 mins elapsed, rate=8.4k fragments per second ||
|| 53% completed, 11 mins elapsed, rate=8.7k fragments per second ||
|| 56% completed, 12 mins elapsed, rate=7.9k fragments per second ||
|| 57% completed, 13 mins elapsed, rate=7.7k fragments per second ||
|| 58% completed, 13 mins elapsed, rate=7.5k fragments per second ||
|| 59% completed, 14 mins elapsed, rate=7.3k fragments per second ||
|| 60% completed, 14 mins elapsed, rate=7.1k fragments per second ||
|| 61% completed, 15 mins elapsed, rate=7.0k fragments per second ||
|| 62% completed, 16 mins elapsed, rate=6.9k fragments per second ||
|| 64% completed, 16 mins elapsed, rate=6.8k fragments per second ||
|| 65% completed, 17 mins elapsed, rate=6.7k fragments per second ||
|| Start read mapping in chunk. ||
|| 66% completed, 18 mins elapsed, rate=6.6k fragments per second ||
|| 72% completed, 19 mins elapsed, rate=6.8k fragments per second ||
|| 79% completed, 20 mins elapsed, rate=6.9k fragments per second ||
|| 86% completed, 21 mins elapsed, rate=7.1k fragments per second ||
|| 89% completed, 23 mins elapsed, rate=6.7k fragments per second ||
|| 90% completed, 23 mins elapsed, rate=6.7k fragments per second ||
|| 91% completed, 24 mins elapsed, rate=6.6k fragments per second ||
|| 92% completed, 25 mins elapsed, rate=6.5k fragments per second ||
|| 93% completed, 25 mins elapsed, rate=6.4k fragments per second ||
|| 94% completed, 26 mins elapsed, rate=6.4k fragments per second ||
|| 96% completed, 26 mins elapsed, rate=6.3k fragments per second ||
|| 97% completed, 27 mins elapsed, rate=6.3k fragments per second ||
|| 98% completed, 27 mins elapsed, rate=6.2k fragments per second ||
|| Start read mapping in chunk. ||
|| 99% completed, 28 mins elapsed, rate=6.2k fragments per second ||
|| 99% completed, 29 mins elapsed, rate=6.0k fragments per second ||
|| 99% completed, 29 mins elapsed, rate=6.0k fragments per second ||
|| 99% completed, 29 mins elapsed, rate=6.0k fragments per second ||
|| 99% completed, 29 mins elapsed, rate=6.0k fragments per second ||
|| 99% completed, 29 mins elapsed, rate=6.0k fragments per second ||
|| 99% completed, 29 mins elapsed, rate=6.0k fragments per second ||
|| 99% completed, 29 mins elapsed, rate=6.0k fragments per second ||
|| 99% completed, 29 mins elapsed, rate=6.0k fragments per second ||
|| 99% completed, 29 mins elapsed, rate=6.0k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total fragments : 10548644 ||
|| Mapped : 10408525 (98.7%) ||
|| Uniquely mapped : 9953382 ||
|| Multi-mapping : 455143 ||
|| ||
|| Unmapped : 140119 ||
|| ||
|| Properly paired : 9361970 ||
|| Not properly paired : 1046555 ||
|| Singleton : 649244 ||
|| Chimeric : 324880 ||
|| Unexpected strandness : 17807 ||
|| Unexpected fragment length : 43860 ||
|| Unexpected read order : 10764 ||
|| ||
|| Indels : 48773 ||
|| ||
|| Running time : 29.2 minutes ||
|| ||
\\============================================================================//#SRR20632989
align(index = "Yeast", readfile1 = "trimmed_SRR20632989_1.fastq", readfile2 = "trimmed_SRR20632989_2.fastq", type = "rna", input_format = "FASTQ", output_format = "BAM", output_file = "SRR20632989.bam", useAnnotation = TRUE, annot.ext = "Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz", isGTF = TRUE, GTF.featureType = "exon", GTF.attrType = "exon_id")
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.12.3
//================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : trimmed_SRR20632989_1.fastq ||
|| Input file 2 : trimmed_SRR20632989_2.fastq ||
|| Output file : SRR20632989.bam (BAM) ||
|| Index name : Yeast ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : yes ||
|| Max alignments per multi-mapping read : 1 ||
|| Annotations : Saccharomyces_cerevisiae.R64-1 ... ||
|| ||
\\============================================================================//
//================= Running (08-May-2023 23:24:31, pid=5328) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [2,37] ||
|| Create the output BAM file. ||
|| Check the index. ||
|| Init the voting space. ||
|| Load the annotation file. ||
|| 7507 annotation records were loaded. ||
|| Global environment is initialised. ||
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
|| 0% completed, 0.4 mins elapsed, rate=13.6k fragments per second ||
|| 6% completed, 1.1 mins elapsed, rate=16.8k fragments per second ||
|| 13% completed, 1.6 mins elapsed, rate=17.0k fragments per second ||
|| 20% completed, 2.2 mins elapsed, rate=17.0k fragments per second ||
|| Estimated fragment length : 203 bp ||
|| 26% completed, 3.5 mins elapsed, rate=11.6k fragments per second ||
|| 28% completed, 3.9 mins elapsed, rate=10.8k fragments per second ||
|| 29% completed, 4.4 mins elapsed, rate=10.3k fragments per second ||
|| 30% completed, 4.8 mins elapsed, rate=9.7k fragments per second ||
|| 32% completed, 5.2 mins elapsed, rate=9.3k fragments per second ||
|| 33% completed, 5.7 mins elapsed, rate=8.9k fragments per second ||
|| 34% completed, 6.1 mins elapsed, rate=8.6k fragments per second ||
|| 35% completed, 6.5 mins elapsed, rate=8.3k fragments per second ||
|| 37% completed, 7.0 mins elapsed, rate=8.1k fragments per second ||
|| Start read mapping in chunk. ||
|| 38% completed, 7.6 mins elapsed, rate=8.1k fragments per second ||
|| 45% completed, 8.5 mins elapsed, rate=8.5k fragments per second ||
|| 52% completed, 9.2 mins elapsed, rate=8.9k fragments per second ||
|| 58% completed, 9 mins elapsed, rate=9.3k fragments per second ||
|| 65% completed, 11 mins elapsed, rate=8.6k fragments per second ||
|| 66% completed, 12 mins elapsed, rate=8.4k fragments per second ||
|| 68% completed, 12 mins elapsed, rate=8.2k fragments per second ||
|| 69% completed, 13 mins elapsed, rate=7.9k fragments per second ||
|| 70% completed, 13 mins elapsed, rate=7.8k fragments per second ||
|| 72% completed, 14 mins elapsed, rate=7.6k fragments per second ||
|| 73% completed, 14 mins elapsed, rate=7.5k fragments per second ||
|| 74% completed, 15 mins elapsed, rate=7.3k fragments per second ||
|| 75% completed, 15 mins elapsed, rate=7.2k fragments per second ||
|| Start read mapping in chunk. ||
|| 77% completed, 16 mins elapsed, rate=7.2k fragments per second ||
|| 83% completed, 17 mins elapsed, rate=7.3k fragments per second ||
|| 90% completed, 18 mins elapsed, rate=7.6k fragments per second ||
|| 93% completed, 19 mins elapsed, rate=7.4k fragments per second ||
|| 93% completed, 19 mins elapsed, rate=7.3k fragments per second ||
|| 94% completed, 19 mins elapsed, rate=7.2k fragments per second ||
|| 95% completed, 20 mins elapsed, rate=7.2k fragments per second ||
|| 96% completed, 20 mins elapsed, rate=7.1k fragments per second ||
|| 96% completed, 20 mins elapsed, rate=7.1k fragments per second ||
|| 97% completed, 21 mins elapsed, rate=7.0k fragments per second ||
|| 98% completed, 21 mins elapsed, rate=7.0k fragments per second ||
|| 99% completed, 21 mins elapsed, rate=6.9k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total fragments : 9052300 ||
|| Mapped : 8939638 (98.8%) ||
|| Uniquely mapped : 8540284 ||
|| Multi-mapping : 399354 ||
|| ||
|| Unmapped : 112662 ||
|| ||
|| Properly paired : 7973593 ||
|| Not properly paired : 966045 ||
|| Singleton : 567809 ||
|| Chimeric : 332735 ||
|| Unexpected strandness : 18150 ||
|| Unexpected fragment length : 38651 ||
|| Unexpected read order : 8700 ||
|| ||
|| Indels : 42165 ||
|| ||
|| Running time : 21.9 minutes ||
|| ||
\\============================================================================//#SRR20632990
align(index = "Yeast", readfile1 = "trimmed_SRR20632990_1.fastq", readfile2 = "trimmed_SRR20632990_2.fastq", type = "rna", input_format = "FASTQ", output_format = "BAM", output_file = "SRR20632990.bam", useAnnotation = TRUE, annot.ext = "Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz", isGTF = TRUE, GTF.featureType = "exon", GTF.attrType = "exon_id")
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.12.3
//================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : trimmed_SRR20632990_1.fastq ||
|| Input file 2 : trimmed_SRR20632990_2.fastq ||
|| Output file : SRR20632990.bam (BAM) ||
|| Index name : Yeast ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : yes ||
|| Max alignments per multi-mapping read : 1 ||
|| Annotations : Saccharomyces_cerevisiae.R64-1 ... ||
|| ||
\\============================================================================//
//================= Running (08-May-2023 23:52:21, pid=5328) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [2,37] ||
|| Create the output BAM file. ||
|| Check the index. ||
|| Init the voting space. ||
|| Load the annotation file. ||
|| 7507 annotation records were loaded. ||
|| Global environment is initialised. ||
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
|| 0% completed, 0.5 mins elapsed, rate=9.8k fragments per second ||
|| 6% completed, 1.2 mins elapsed, rate=16.3k fragments per second ||
|| 13% completed, 1.9 mins elapsed, rate=16.2k fragments per second ||
|| 20% completed, 2.5 mins elapsed, rate=16.4k fragments per second ||
|| Estimated fragment length : 203 bp ||
|| 25% completed, 3.6 mins elapsed, rate=11.2k fragments per second ||
|| 26% completed, 4.1 mins elapsed, rate=10.5k fragments per second ||
|| 27% completed, 4.5 mins elapsed, rate=10.0k fragments per second ||
|| 28% completed, 4.9 mins elapsed, rate=9.4k fragments per second ||
|| 30% completed, 5.4 mins elapsed, rate=9.1k fragments per second ||
|| 31% completed, 5.8 mins elapsed, rate=8.8k fragments per second ||
|| 32% completed, 6.2 mins elapsed, rate=8.5k fragments per second ||
|| 33% completed, 6.6 mins elapsed, rate=8.3k fragments per second ||
|| 34% completed, 7.0 mins elapsed, rate=8.1k fragments per second ||
|| Start read mapping in chunk. ||
|| 36% completed, 7.6 mins elapsed, rate=8.3k fragments per second ||
|| 42% completed, 8.6 mins elapsed, rate=8.6k fragments per second ||
|| 49% completed, 9.3 mins elapsed, rate=9.1k fragments per second ||
|| 56% completed, 10 mins elapsed, rate=9.6k fragments per second ||
|| 61% completed, 11 mins elapsed, rate=8.9k fragments per second ||
|| 62% completed, 11 mins elapsed, rate=8.6k fragments per second ||
|| 63% completed, 12 mins elapsed, rate=8.4k fragments per second ||
|| 64% completed, 12 mins elapsed, rate=8.3k fragments per second ||
|| 66% completed, 13 mins elapsed, rate=8.1k fragments per second ||
|| 67% completed, 13 mins elapsed, rate=8.0k fragments per second ||
|| 68% completed, 14 mins elapsed, rate=7.8k fragments per second ||
|| 69% completed, 14 mins elapsed, rate=7.7k fragments per second ||
|| 70% completed, 15 mins elapsed, rate=7.5k fragments per second ||
|| Start read mapping in chunk. ||
|| 72% completed, 15 mins elapsed, rate=7.6k fragments per second ||
|| 78% completed, 16 mins elapsed, rate=7.8k fragments per second ||
|| 85% completed, 17 mins elapsed, rate=8.1k fragments per second ||
|| 91% completed, 18 mins elapsed, rate=8.0k fragments per second ||
|| 92% completed, 19 mins elapsed, rate=7.9k fragments per second ||
|| 93% completed, 19 mins elapsed, rate=7.8k fragments per second ||
|| 94% completed, 19 mins elapsed, rate=7.7k fragments per second ||
|| 95% completed, 20 mins elapsed, rate=7.6k fragments per second ||
|| 96% completed, 20 mins elapsed, rate=7.5k fragments per second ||
|| 97% completed, 21 mins elapsed, rate=7.4k fragments per second ||
|| 98% completed, 21 mins elapsed, rate=7.3k fragments per second ||
|| 99% completed, 22 mins elapsed, rate=7.2k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total fragments : 9684741 ||
|| Mapped : 9559930 (98.7%) ||
|| Uniquely mapped : 9107267 ||
|| Multi-mapping : 452663 ||
|| ||
|| Unmapped : 124811 ||
|| ||
|| Properly paired : 8566353 ||
|| Not properly paired : 993577 ||
|| Singleton : 612134 ||
|| Chimeric : 309271 ||
|| Unexpected strandness : 17525 ||
|| Unexpected fragment length : 45052 ||
|| Unexpected read order : 9595 ||
|| ||
|| Indels : 44181 ||
|| ||
|| Running time : 22.5 minutes ||
|| ||
\\============================================================================//#SRR20632991
align(index = "Yeast", readfile1 = "trimmed_SRR20632991_1.fastq", readfile2 = "trimmed_SRR20632991_2.fastq", type = "rna", input_format = "FASTQ", output_format = "BAM", output_file = "SRR20632991.bam", useAnnotation = TRUE, annot.ext = "Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz", isGTF = TRUE, GTF.featureType = "exon", GTF.attrType = "exon_id")
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.12.3
//================================= setting ==================================\\
|| ||
|| Function : Read alignment (RNA-Seq) ||
|| Input file 1 : trimmed_SRR20632991_1.fastq ||
|| Input file 2 : trimmed_SRR20632991_2.fastq ||
|| Output file : SRR20632991.bam (BAM) ||
|| Index name : Yeast ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| # of extracted subreads : 10 ||
|| Min read1 vote : 3 ||
|| Min read2 vote : 1 ||
|| Max fragment size : 600 ||
|| Min fragment size : 50 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : yes ||
|| Max alignments per multi-mapping read : 1 ||
|| Annotations : Saccharomyces_cerevisiae.R64-1 ... ||
|| ||
\\============================================================================//
//================= Running (09-May-2023 00:20:50, pid=5328) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| The range of Phred scores observed in the data is [2,37] ||
|| Create the output BAM file. ||
|| Check the index. ||
|| Init the voting space. ||
|| Load the annotation file. ||
|| 7507 annotation records were loaded. ||
|| Global environment is initialised. ||
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
|| 0% completed, 460 mins elapsed, rate=1.1k fragments per second ||
|| 6% completed, 461 mins elapsed, rate=9.5k fragments per second ||
|| 13% completed, 462 mins elapsed, rate=10.9k fragments per second ||
|| 20% completed, 463 mins elapsed, rate=11.7k fragments per second ||
|| Estimated fragment length : 205 bp ||
|| 26% completed, 464 mins elapsed, rate=0.1k fragments per second ||
|| 27% completed, 464 mins elapsed, rate=0.1k fragments per second ||
|| 28% completed, 465 mins elapsed, rate=0.1k fragments per second ||
|| 29% completed, 465 mins elapsed, rate=0.1k fragments per second ||
|| 31% completed, 466 mins elapsed, rate=0.1k fragments per second ||
|| 32% completed, 466 mins elapsed, rate=0.1k fragments per second ||
|| 33% completed, 467 mins elapsed, rate=0.1k fragments per second ||
|| 34% completed, 467 mins elapsed, rate=0.1k fragments per second ||
|| 36% completed, 468 mins elapsed, rate=0.1k fragments per second ||
|| Start read mapping in chunk. ||
|| 37% completed, 469 mins elapsed, rate=6.3k fragments per second ||
|| 44% completed, 471 mins elapsed, rate=6.3k fragments per second ||
|| 50% completed, 472 mins elapsed, rate=6.7k fragments per second ||
|| 57% completed, 473 mins elapsed, rate=7.0k fragments per second ||
|| 63% completed, 474 mins elapsed, rate=0.2k fragments per second ||
|| 64% completed, 475 mins elapsed, rate=0.2k fragments per second ||
|| 66% completed, 476 mins elapsed, rate=0.2k fragments per second ||
|| 67% completed, 477 mins elapsed, rate=0.2k fragments per second ||
|| 68% completed, 477 mins elapsed, rate=0.2k fragments per second ||
|| 69% completed, 478 mins elapsed, rate=0.2k fragments per second ||Error in file(out, "wt") : cannot open the connection|| 71% completed, 479 mins elapsed, rate=0.2k fragments per second ||
|| 72% completed, 480 mins elapsed, rate=0.2k fragments per second ||Error in file(out, "wt") : cannot open the connection|| 73% completed, 481 mins elapsed, rate=0.2k fragments per second ||
|| Start read mapping in chunk. ||
|| 75% completed, 483 mins elapsed, rate=5.1k fragments per second ||
|| 81% completed, 484 mins elapsed, rate=5.2k fragments per second ||
|| 88% completed, 485 mins elapsed, rate=5.4k fragments per second ||
|| 92% completed, 487 mins elapsed, rate=0.3k fragments per second ||
|| 93% completed, 487 mins elapsed, rate=0.3k fragments per second ||
|| 94% completed, 488 mins elapsed, rate=0.3k fragments per second ||
|| 94% completed, 488 mins elapsed, rate=0.3k fragments per second ||
|| 95% completed, 489 mins elapsed, rate=0.3k fragments per second ||
|| 96% completed, 489 mins elapsed, rate=0.3k fragments per second ||
|| 97% completed, 490 mins elapsed, rate=0.3k fragments per second ||
|| 98% completed, 490 mins elapsed, rate=0.3k fragments per second ||
|| 99% completed, 491 mins elapsed, rate=0.3k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total fragments : 9325312 ||
|| Mapped : 9200338 (98.7%) ||
|| Uniquely mapped : 8766392 ||
|| Multi-mapping : 433946 ||
|| ||
|| Unmapped : 124974 ||
|| ||
|| Properly paired : 8329689 ||
|| Not properly paired : 870649 ||
|| Singleton : 590668 ||
|| Chimeric : 223175 ||
|| Unexpected strandness : 12755 ||
|| Unexpected fragment length : 33804 ||
|| Unexpected read order : 10247 ||
|| ||
|| Indels : 44349 ||
|| ||
|| Running time : 491.6 minutes ||
|| ||
\\============================================================================//##Read counts on a single sample
SRR20632986_counts <- featureCounts(files = "SRR20632986.bam", annot.ext = "Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz", isGTFAnnotationFile = TRUE, GTF.featureType = "exon", GTF.attrType = "exon_id", useMetaFeatures = TRUE, countMultiMappingReads = TRUE, juncCounts = TRUE, genome = "Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz", isPairedEnd = TRUE, requireBothEndsMapped = TRUE, checkFragLength = TRUE, countChimericFragments = TRUE)
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.12.3
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| ||
|| SRR20632986.bam ||
|| ||
|| Paired-end : yes ||
|| Count read pairs : yes ||
|| Annotation : Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz ... ||
|| Dir for temp files : . ||
|| Junction Counting : <output_file>.jcounts ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz ... ||
|| Features : 7507 ||
|| Meta-features : 7507 ||
|| Chromosomes/contigs : 17 ||
|| ||
|| Load FASTA contigs from Saccharomyces_cerevisiae.R64-1-1.dna.toplevel. ... ||
|| 16 contigs were loaded ||
|| ||
|| Process BAM file SRR20632986.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 14070993 ||
|| Successfully assigned alignments : 12146601 (86.3%) ||
|| Running time : 0.73 minutes ||
|| ||
|| Write the final count table. ||
|| Write the junction count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//#Checking counts file
names(SRR20632986_counts)[1] "counts" "counts_junction" "annotation"
[4] "targets" "stat" SRR20632986_counts$targets[1] "SRR20632986.bam"SRR20632986_counts$statdim(SRR20632986_counts$counts)[1] 7507 1head(SRR20632986_counts$counts) SRR20632986.bam
YAL069W_mRNA-E1 0
YAL068W-A_mRNA-E1 0
YAL068C_mRNA-E1 0
YAL067W-A_mRNA-E1 0
YAL067C_mRNA-E1 90
YAL066W_mRNA-E1 1head(SRR20632986_counts$annotation, n=20L)##Feature counts on multiple samples at once (loaded all mapped bam files into directory to complete) #create a value to address all bam files at once
bams <- list.files(pattern = ".bam$")#Check all of the correct bam files are included and in order
head(bams, n=10L)[1] "SRR20632986.bam" "SRR20632987.bam" "SRR20632988.bam" "SRR20632989.bam"
[5] "SRR20632990.bam" "SRR20632991.bam"#Running read counts on all samples at once
Yeast_counts <- featureCounts(files = bams, annot.ext = "Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz", isGTFAnnotationFile = TRUE, GTF.featureType = "exon", GTF.attrType = "exon_id", useMetaFeatures = TRUE, countMultiMappingReads = TRUE, juncCounts = TRUE, genome = "Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz", isPairedEnd = TRUE, requireBothEndsMapped = TRUE, checkFragLength = TRUE, countChimericFragments = TRUE)
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.12.3
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 6 BAM files ||
|| ||
|| SRR20632986.bam ||
|| SRR20632987.bam ||
|| SRR20632988.bam ||
|| SRR20632989.bam ||
|| SRR20632990.bam ||
|| SRR20632991.bam ||
|| ||
|| Paired-end : yes ||
|| Count read pairs : yes ||
|| Annotation : Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz ... ||
|| Dir for temp files : . ||
|| Junction Counting : <output_file>.jcounts ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz ... ||
|| Features : 7507 ||
|| Meta-features : 7507 ||
|| Chromosomes/contigs : 17 ||
|| ||
|| Load FASTA contigs from Saccharomyces_cerevisiae.R64-1-1.dna.toplevel. ... ||
|| 16 contigs were loaded ||
|| ||
|| Process BAM file SRR20632986.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 14070993 ||
|| Successfully assigned alignments : 12146601 (86.3%) ||
|| Running time : 0.84 minutes ||
|| ||
|| Process BAM file SRR20632987.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 10321097 ||
|| Successfully assigned alignments : 8953189 (86.7%) ||
|| Running time : 0.66 minutes ||
|| ||
|| Process BAM file SRR20632988.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 10548644 ||
|| Successfully assigned alignments : 8709162 (82.6%) ||
|| Running time : 0.82 minutes ||
|| ||
|| Process BAM file SRR20632989.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 9052300 ||
|| Successfully assigned alignments : 7408286 (81.8%) ||
|| Running time : 0.69 minutes ||
|| ||
|| Process BAM file SRR20632990.bam... ||Warning in gzfile(file, mode) :
cannot open compressed file 'C:\Users\benfu\AppData\Local\Temp\RtmpgZ6VSS\rstudio-available-packages-14d0498849d7/time.rds', probable reason 'No such file or directory'
Error in gzfile(file, mode) : cannot open the connection|| Paired-end reads are included. ||
|| Total alignments : 9684741 ||
|| Successfully assigned alignments : 7983163 (82.4%) ||
|| Running time : 0.69 minutes ||
|| ||
|| Process BAM file SRR20632991.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 9325312 ||
|| Successfully assigned alignments : 7753669 (83.1%) ||
|| Running time : 0.67 minutes ||
|| ||
|| Write the final count table. ||
|| Write the junction count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//Warning in png(..., res = dpi, units = "in") :
unable to open file 'C:\Users\benfu\AppData\Local\Temp\RtmpgZ6VSS\file14d051bdf49' for writing
Warning in png(..., res = dpi, units = "in") : opening device failed
Warning in (function (filename = if (onefile) "Rplots.svg" else "Rplot%03d.svg", :
cairo error 'error while writing to output stream'
Quitting from lines 8-9 (Saccharomyces_cerevisiae_RNAseq_analysis.Rmd) #Checking multiple read counts output
names(Yeast_counts)[1] "counts" "counts_junction" "annotation"
[4] "targets" "stat" dim(Yeast_counts$counts)[1] 7507 6head(Yeast_counts$counts) SRR20632986.bam SRR20632987.bam
YAL069W_mRNA-E1 0 0
YAL068W-A_mRNA-E1 0 0
YAL068C_mRNA-E1 0 0
YAL067W-A_mRNA-E1 0 0
YAL067C_mRNA-E1 90 59
YAL066W_mRNA-E1 1 0
SRR20632988.bam SRR20632989.bam
YAL069W_mRNA-E1 0 0
YAL068W-A_mRNA-E1 0 0
YAL068C_mRNA-E1 0 0
YAL067W-A_mRNA-E1 0 1
YAL067C_mRNA-E1 49 20
YAL066W_mRNA-E1 1 0
SRR20632990.bam SRR20632991.bam
YAL069W_mRNA-E1 0 0
YAL068W-A_mRNA-E1 0 0
YAL068C_mRNA-E1 2 1
YAL067W-A_mRNA-E1 1 1
YAL067C_mRNA-E1 50 41
YAL066W_mRNA-E1 0 0head(Yeast_counts$annotation)tail(Yeast_counts$annotation)##Differential expression with DESeq2 #Create a comma separated value (.csv) file in excel with sample bam files in the same order as the collective bam file created earlier and list WT or mct1 as required
head(Yeast_counts$counts) SRR20632986.bam SRR20632987.bam SRR20632988.bam SRR20632989.bam SRR20632990.bam
YAL069W_mRNA-E1 0 0 0 0 0
YAL068W-A_mRNA-E1 0 0 0 0 0
YAL068C_mRNA-E1 0 0 0 0 2
YAL067W-A_mRNA-E1 0 0 0 1 1
YAL067C_mRNA-E1 90 59 49 20 50
YAL066W_mRNA-E1 1 0 1 0 0
SRR20632991.bam
YAL069W_mRNA-E1 0
YAL068W-A_mRNA-E1 0
YAL068C_mRNA-E1 1
YAL067W-A_mRNA-E1 1
YAL067C_mRNA-E1 41
YAL066W_mRNA-E1 0#Create a counts matrix
head(Yeast_counts$annotation)#Install DESeq2
tail(Yeast_counts$annotation)#Load DESeq2
library(DESeq2)Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
anyDuplicated, aperm, append, as.data.frame, basename,
cbind, colnames, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted,
lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
expand.grid, I, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins,
colOrderStats, colProds, colQuantiles, colRanges, colRanks,
colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs,
colVars, colWeightedMads, colWeightedMeans,
colWeightedMedians, colWeightedSds, colWeightedVars,
rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse,
rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums,
rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs,
rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs,
rowVars, rowWeightedMads, rowWeightedMeans,
rowWeightedMedians, rowWeightedSds, rowWeightedVars
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages
'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians#Converting the counts matrix into a DESeq2 Data Set
Yeast_dds <- DESeqDataSetFromMatrix(countData = Yeast_counts_matrix, colData = YeastSamples, design = ~ condition)Warning: some variables in design formula are characters, converting to factors#Retrieved this error: Error in SummarizedExperiment(assays = SimpleList(counts = countData), : the rownames and colnames of the supplied assay(s) must be NULL or identical to those of the SummarizedExperiment object (or derivative) to construct #Error was fixed by correcting the csv file SRR20632** -> SRR206329** (all SRR file names were missing a 9)
#Check Yeast_dds file
Yeast_ddsclass: DESeqDataSet
dim: 7507 6
metadata(1): version
assays(1): counts
rownames(7507): YAL069W_mRNA-E1 YAL068W-A_mRNA-E1 ... YPR204W_mRNA-E1
YPR204C-A_mRNA-E1
rowData names(0):
colnames(6): SRR20632986.bam SRR20632987.bam ... SRR20632990.bam
SRR20632991.bam
colData names(1): condition#Set the condition for all other conditions to be compared to
Yeast_dds$condition <- relevel(Yeast_dds$condition, ref = "WT")#Remove data of genes that with no expression (0), (i.e. “keep” all rows with values above 1)
keep <- rowSums(counts(Yeast_dds)) >1
Yeast_dds <- Yeast_dds[keep,]#Check to see if any rows were removed (7507 -> 6921 rows is a 586 reduction, i.e. 586 genes with no expression)
dim(Yeast_dds)[1] 6921 6#Create the rlog normalisation for the samples
Yeast_rlog <- rlog(Yeast_dds, blind = TRUE)#Plot result
plot(assay(Yeast_rlog) [,1:2], pch=16, cex=0.3)
plot(assay(Yeast_rlog) [,3:4], pch=16, cex=0.3)
plot(assay(Yeast_rlog) [,5:6], pch=16, cex=0.3)
#Installing heatmap generation tools
BiocManager::install("pheatmap")'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.3 (2023-03-15 ucrt)
Warning: package(s) not installed when version(s) same as or greater than current; use `force =
TRUE` to re-install: 'pheatmap'Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.2.3/library
packages:
class, KernSmooth, lattice, MASS, Matrix, nnet, survival
Old packages: 'DelayedArray'Update all/some/none? [a/s/n]: aWarning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'
There is a binary version available but the source version is later:
Binaries will be installedtrying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/DelayedArray_0.23.2.zip'
Content type 'application/zip' length 2449113 bytes (2.3 MB)
downloaded 2.3 MBpackage ‘DelayedArray’ successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package ‘DelayedArray’Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\DelayedArray\libs\x64\DelayedArray.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\DelayedArray\libs\x64\DelayedArray.dll: Permission deniedWarning: restored ‘DelayedArray’
The downloaded binary packages are in
C:\Users\benfu\AppData\Local\Temp\RtmpK4OWss\downloaded_packagesBiocManager::install("RcolorBrewer")'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.3 (2023-03-15 ucrt)
Installing package(s) 'RcolorBrewer'
Warning: package ‘RcolorBrewer’ is not available for Bioconductor version '3.16'
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packagesWarning: Perhaps you meant ‘RColorBrewer’ ?Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.2.3/library
packages:
class, KernSmooth, lattice, MASS, Matrix, nnet, survival
Old packages: 'DelayedArray'Update all/some/none? [a/s/n]: aWarning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'
There is a binary version available but the source version is later:
Binaries will be installedtrying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/DelayedArray_0.23.2.zip'
Content type 'application/zip' length 2449113 bytes (2.3 MB)
downloaded 2.3 MBpackage ‘DelayedArray’ successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package ‘DelayedArray’Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\DelayedArray\libs\x64\DelayedArray.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\DelayedArray\libs\x64\DelayedArray.dll: Permission deniedWarning: restored ‘DelayedArray’
The downloaded binary packages are in
C:\Users\benfu\AppData\Local\Temp\RtmpK4OWss\downloaded_packages#Loading heatmap tools
library(pheatmap)
library(RColorBrewer)#Creating the distance matrix
Yeast_sampleDist <- dist(t(assay(Yeast_rlog)))
Yeast_sampleDist SRR20632986.bam SRR20632987.bam SRR20632988.bam SRR20632989.bam SRR20632990.bam
SRR20632987.bam 24.320350
SRR20632988.bam 18.433080 9.430259
SRR20632989.bam 21.915905 13.805577 13.372241
SRR20632990.bam 15.530746 27.036702 22.336196 21.075996
SRR20632991.bam 15.633508 27.603943 22.895206 21.881963 6.878317#Heatmap of sample distances
Yeast_sampleDistMatrix <- as.matrix(Yeast_sampleDist)
row.names(Yeast_sampleDistMatrix) <- paste(Yeast_rlog$condition, Yeast_rlog$sizeFactor, sep = "-")
colnames(Yeast_sampleDistMatrix) <- NULL
colours <- colorRampPalette(rev(brewer.pal(9, "Blues")))(255)
pheatmap(Yeast_sampleDistMatrix, clustering_distance_rows = Yeast_sampleDist, clustering_distance_cols = Yeast_sampleDist, color = colours)
#Creating a Principal components analysis (PCA) plot
plotPCA(Yeast_rlog)
#Calculating differentially expressed genes
YeastDDS_DE <- DESeq(Yeast_dds)estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testingYeast_res <- results(YeastDDS_DE)
Yeast_reslog2 fold change (MLE): condition mct1 vs WT
Wald test p-value: condition mct1 vs WT
DataFrame with 6921 rows and 6 columns
baseMean log2FoldChange lfcSE stat
<numeric> <numeric> <numeric> <numeric>
YAL068C_mRNA-E1 0.585912 -2.909177 2.885011 -1.008376
YAL067W-A_mRNA-E1 0.585574 -2.908499 2.304304 -1.262203
YAL067C_mRNA-E1 49.061683 0.340579 0.384406 0.885988
YAL066W_mRNA-E1 0.278321 1.371278 3.574854 0.383590
YAL065C_mRNA-E1 5.920620 1.250661 0.732944 1.706353
... ... ... ... ...
YPR201W_mRNA-E1 67.8290 0.461758 0.223933 2.062037
YPR202W_mRNA-E1 16.1510 0.369108 0.446293 0.827053
YPR202W_mRNA-E2 49.7788 0.166732 0.294720 0.565732
YPR203W_mRNA-E1 36.0672 0.317818 0.353521 0.899008
YPR204W_mRNA-E1 1028.2677 0.080264 0.257345 0.311893
pvalue padj
<numeric> <numeric>
YAL068C_mRNA-E1 0.3132739 NA
YAL067W-A_mRNA-E1 0.2068757 NA
YAL067C_mRNA-E1 0.3756242 0.766803
YAL066W_mRNA-E1 0.7012824 NA
YAL065C_mRNA-E1 0.0879423 0.494336
... ... ...
YPR201W_mRNA-E1 0.0392042 0.351441
YPR202W_mRNA-E1 0.4082068 0.773955
YPR202W_mRNA-E2 0.5715760 0.845895
YPR203W_mRNA-E1 0.3686486 0.761664
YPR204W_mRNA-E1 0.7551220 0.918878mcols(Yeast_res, use.names = TRUE)DataFrame with 6 rows and 2 columns
type description
<character> <character>
baseMean intermediate mean of normalized c..
log2FoldChange results log2 fold change (ML..
lfcSE results standard error: cond..
stat results Wald statistic: cond..
pvalue results Wald test p-value: c..
padj results BH adjusted p-values#Examining the results
summary(Yeast_res)
out of 6921 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up) : 152, 2.2%
LFC < 0 (down) : 78, 1.1%
outliers [1] : 4, 0.058%
low counts [2] : 537, 7.8%
(mean count < 3)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results#Finding the number of adjusted p-values < 0.1
sum(Yeast_res$padj < 0.1, na.rm = TRUE)[1] 230#Changing the adjusted p-value cutoff to 0.05 (reset false discovery rate)
Yeast_res_5 <- results(YeastDDS_DE, alpha = 0.05)
table(Yeast_res_5$padj < 0.05)
FALSE TRUE
6072 174 #Examine results with reduced adjusted p-value cutoff
summary(Yeast_res_5)
out of 6921 with nonzero total read count
adjusted p-value < 0.05
LFC > 0 (up) : 119, 1.7%
LFC < 0 (down) : 55, 0.79%
outliers [1] : 4, 0.058%
low counts [2] : 671, 9.7%
(mean count < 6)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results#Ordering results table by smallest p-value and adjusted p-value, respectively
Yeast_res_ordered <- Yeast_res[order(Yeast_res$pvalue),]
Yeast_res_ordpadj <- Yeast_res[order(Yeast_res$padj),]##Viewing and comparing results, ordered results (p-value) and ordered results (adjusted p-value) #Heads
head(Yeast_res)log2 fold change (MLE): condition mct1 vs WT
Wald test p-value: condition mct1 vs WT
DataFrame with 6 rows and 6 columns
baseMean log2FoldChange lfcSE stat pvalue padj
<numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
YAL068C_mRNA-E1 0.585912 -2.909177 2.885011 -1.008376 0.3132739 NA
YAL067W-A_mRNA-E1 0.585574 -2.908499 2.304304 -1.262203 0.2068757 NA
YAL067C_mRNA-E1 49.061683 0.340579 0.384406 0.885988 0.3756242 0.766803
YAL066W_mRNA-E1 0.278321 1.371278 3.574854 0.383590 0.7012824 NA
YAL065C_mRNA-E1 5.920620 1.250661 0.732944 1.706353 0.0879423 0.494336
YAL064W-B_mRNA-E1 6.517108 0.839925 0.714585 1.175404 0.2398333 0.679322head(Yeast_res_ordered)log2 fold change (MLE): condition mct1 vs WT
Wald test p-value: condition mct1 vs WT
DataFrame with 6 rows and 6 columns
baseMean log2FoldChange lfcSE stat pvalue padj
<numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
YOR153W_mRNA-E1 15546.178 1.91405 0.113651 16.8415 1.21187e-63 7.73170e-60
YGL009C_mRNA-E1 3799.353 -2.03344 0.173800 -11.6999 1.27620e-31 2.93213e-28
YLR303W_mRNA-E1 1756.881 13.99367 1.196723 11.6933 1.37874e-31 2.93213e-28
YMR102C_mRNA-E1 1126.985 1.17140 0.100539 11.6512 2.26337e-31 3.61007e-28
YBR115C_mRNA-E1 618.027 -12.95213 1.186565 -10.9157 9.70263e-28 1.23806e-24
YBR047W_mRNA-E1 121.597 2.43760 0.241437 10.0962 5.74190e-24 6.10555e-21head(Yeast_res_ordpadj)log2 fold change (MLE): condition mct1 vs WT
Wald test p-value: condition mct1 vs WT
DataFrame with 6 rows and 6 columns
baseMean log2FoldChange lfcSE stat pvalue padj
<numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
YOR153W_mRNA-E1 15546.178 1.91405 0.113651 16.8415 1.21187e-63 7.73170e-60
YGL009C_mRNA-E1 3799.353 -2.03344 0.173800 -11.6999 1.27620e-31 2.93213e-28
YLR303W_mRNA-E1 1756.881 13.99367 1.196723 11.6933 1.37874e-31 2.93213e-28
YMR102C_mRNA-E1 1126.985 1.17140 0.100539 11.6512 2.26337e-31 3.61007e-28
YBR115C_mRNA-E1 618.027 -12.95213 1.186565 -10.9157 9.70263e-28 1.23806e-24
YBR047W_mRNA-E1 121.597 2.43760 0.241437 10.0962 5.74190e-24 6.10555e-21#Tails
tail(Yeast_res)log2 fold change (MLE): condition mct1 vs WT
Wald test p-value: condition mct1 vs WT
DataFrame with 6 rows and 6 columns
baseMean log2FoldChange lfcSE stat pvalue padj
<numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
YPR200C_mRNA-E1 42.7891 0.497340 0.311088 1.598711 0.1098848 0.532320
YPR201W_mRNA-E1 67.8290 0.461758 0.223933 2.062037 0.0392042 0.351441
YPR202W_mRNA-E1 16.1510 0.369108 0.446293 0.827053 0.4082068 0.773955
YPR202W_mRNA-E2 49.7788 0.166732 0.294720 0.565732 0.5715760 0.845895
YPR203W_mRNA-E1 36.0672 0.317818 0.353521 0.899008 0.3686486 0.761664
YPR204W_mRNA-E1 1028.2677 0.080264 0.257345 0.311893 0.7551220 0.918878tail(Yeast_res_ordered)log2 fold change (MLE): condition mct1 vs WT
Wald test p-value: condition mct1 vs WT
DataFrame with 6 rows and 6 columns
baseMean log2FoldChange lfcSE stat pvalue padj
<numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
YNL004W_mRNA-E1 25.3420 9.58309e-05 0.385824 0.000248380 0.999802 0.999842
YPR123C_mRNA-E1 14.7763 1.06657e-04 0.538905 0.000197913 0.999842 0.999842
YDL075W_mRNA-E1 351.0642 -1.46841e+00 1.226051 -1.197675258 NA NA
YDR342C_mRNA-E1 290.6640 -9.71410e-01 1.472269 -0.659804593 NA NA
YDR343C_mRNA-E1 1405.3249 -6.87335e-01 1.156855 -0.594141195 NA NA
YHR137W_mRNA-E1 46.3582 -1.65335e-01 1.386532 -0.119243580 NA NAtail(Yeast_res_ordpadj)log2 fold change (MLE): condition mct1 vs WT
Wald test p-value: condition mct1 vs WT
DataFrame with 6 rows and 6 columns
baseMean log2FoldChange lfcSE stat pvalue padj
<numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
YPR142C_mRNA-E1 0.389341 -2.320176 4.03805 -0.5745788 0.565576 NA
tI(AAU)P1_tRNA-E1 0.342255 -0.465815 3.40307 -0.1368806 0.891125 NA
YPR153W_mRNA-E1 1.847577 -0.764619 1.38381 -0.5525469 0.580574 NA
tA(AGC)P_tRNA-E1 1.104728 -0.161049 2.15177 -0.0748451 0.940338 NA
YPR187W_mRNA-E1 0.628610 1.037357 2.37081 0.4375531 0.661710 NA
YPR197C_mRNA-E1 0.709839 -1.949977 2.30435 -0.8462143 0.397433 NA#Visualisation of differentially expressed genes with an MA plot
plotMA(Yeast_res, ylim=c(-5,5))
#Checking the names in the differential expression file
resultsNames(YeastDDS_DE)[1] "Intercept" "condition_mct1_vs_WT"#Installing apeglm package
#Load apeglm
#Creating log fold change on the results of differential expression
Yeast_resLFC <- lfcShrink(YeastDDS_DE, coef = "condition_mct1_vs_WT", type = "apeglm")using 'apeglm' for LFC shrinkage. If used in published research, please cite:
Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
sequence count data: removing the noise and preserving large differences.
Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895#check file
Yeast_resLFClog2 fold change (MAP): condition mct1 vs WT
Wald test p-value: condition mct1 vs WT
DataFrame with 6921 rows and 5 columns
baseMean log2FoldChange lfcSE pvalue padj
<numeric> <numeric> <numeric> <numeric> <numeric>
YAL068C_mRNA-E1 0.585912 -0.00517948 0.122521 0.3132739 NA
YAL067W-A_mRNA-E1 0.585574 -0.00802470 0.122693 0.2068757 NA
YAL067C_mRNA-E1 49.061683 0.03248266 0.122317 0.3756242 0.766803
YAL066W_mRNA-E1 0.278321 0.00267398 0.122414 0.7012824 NA
YAL065C_mRNA-E1 5.920620 0.03746028 0.129002 0.0879423 0.494336
... ... ... ... ... ...
YPR201W_mRNA-E1 67.8290 0.1737475 0.223685 0.0392042 0.351441
YPR202W_mRNA-E1 16.1510 0.0265569 0.121921 0.4082068 0.773955
YPR202W_mRNA-E2 49.7788 0.0250693 0.116084 0.5715760 0.845895
YPR203W_mRNA-E1 36.0672 0.0353459 0.122217 0.3686486 0.761664
YPR204W_mRNA-E1 1028.2677 0.0145618 0.111498 0.7551220 0.918878#MA plot of log fold change
plotMA(Yeast_resLFC, ylim=c(-10,10))
#Finding genes with expressions more than doubled or halved the original
Yeast_resLFC1 <- results(YeastDDS_DE, lfcThreshold = 1)table(Yeast_resLFC1$padj < 0.01)
FALSE TRUE
6909 8 #Finding the highest adjusted p-value where all results are false
table(Yeast_resLFC1$padj < 1E-22)
FALSE TRUE
6916 1 table(Yeast_resLFC1$padj < 1E-23)
FALSE
6917 #MA plot of genes with expressions more than doubled or halved the original
plotMA(Yeast_resLFC1, ylim=c(-10,10))
#Genes with a false discovery rate less than 5%
Yeast_res_5sub <- subset(Yeast_res, padj < 0.05)#Head
head(Yeast_res_5sub[order(Yeast_res_5sub$log2FoldChange),])log2 fold change (MLE): condition mct1 vs WT
Wald test p-value: condition mct1 vs WT
DataFrame with 6 rows and 6 columns
baseMean log2FoldChange lfcSE stat pvalue
<numeric> <numeric> <numeric> <numeric> <numeric>
YBR115C_mRNA-E1 618.0275 -12.95213 1.186565 -10.91566 9.70263e-28
YJL153C_mRNA-E1 871.3070 -3.45969 1.035288 -3.34177 8.32467e-04
YGL009C_mRNA-E1 3799.3525 -2.03344 0.173800 -11.69989 1.27620e-31
YOR273C_mRNA-E1 869.9086 -1.78403 0.341498 -5.22414 1.74963e-07
snR17b_snoRNA-E2 32.8773 -1.70117 0.428865 -3.96669 7.28789e-05
YEL073C_mRNA-E1 228.5888 -1.59072 0.462919 -3.43628 5.89761e-04
padj
<numeric>
YBR115C_mRNA-E1 1.23806e-24
YJL153C_mRNA-E1 3.37544e-02
YGL009C_mRNA-E1 2.93213e-28
YOR273C_mRNA-E1 3.72087e-05
snR17b_snoRNA-E2 5.81209e-03
YEL073C_mRNA-E1 2.70696e-02#MA plot of the genes with a false discovery rate less than 5%
plotMA(Yeast_res_5sub, ylim=c(-10,10))
#MA plot of all the genes
plotMA(Yeast_res, ylim=c(-10,10))
#Visualisation of the counts for the gene with the smallest adjusted p-value
plotCounts(Yeast_dds, gene = which.min(Yeast_res$padj), intgroup = "condition")
#Visualisation of the counts for the gene with the largest adjusted p-value
plotCounts(Yeast_dds, gene = which.max(Yeast_res$padj), intgroup = "condition")
#Visualisation of the counts for the YAL067W-A_mRNA-E1 gene
plotCounts(Yeast_dds, "YAL067W-A_mRNA-E1", intgroup = "condition", xlab = "Group")
#Visualisation of the counts for the YOR221C_mRNA-E1 gene
plotCounts(Yeast_dds, "YOR221C_mRNA-E1", intgroup = "condition", xlab = "Group")
#Installing ComplexHeatmap tool
#Loading ComplexHeatmap
library(ComplexHeatmap)Loading required package: grid
========================================
ComplexHeatmap version 2.14.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
genomic data. Bioinformatics 2016.
The new InteractiveComplexHeatmap package can directly export static
complex heatmaps into an interactive Shiny app with zero effort. Have a try!
This message can be suppressed by:
suppressPackageStartupMessages(library(ComplexHeatmap))
========================================
! pheatmap() has been masked by ComplexHeatmap::pheatmap(). Most of the arguments
in the original pheatmap() are identically supported in the new function. You
can still use the original function by explicitly calling pheatmap::pheatmap().
Attaching package: 'ComplexHeatmap'
The following object is masked from 'package:pheatmap':
pheatmap#Creating a heatmap of the highest 20 log2fold change genes
Yeast_top20 <- order(Yeast_resLFC$log2FoldChange, decreasing = TRUE) [1:20]
pheatmap(assay(Yeast_rlog)[Yeast_top20, ], cluster_rows = TRUE, show_rownames = TRUE, cluster_cols = FALSE)
#Creating a heatmap of the lowest 20 log2fold change genes
Yeast_bottom20 <- order(Yeast_resLFC$log2FoldChange, decreasing = FALSE) [1:20]
pheatmap(assay(Yeast_rlog)[Yeast_bottom20, ], cluster_rows = TRUE, show_rownames = TRUE, cluster_cols = FALSE)
#Creating a heatmap of the highest 20 expressing genes
Yeast_highest20 <- order(Yeast_resLFC$baseMean, decreasing = TRUE) [1:20]
pheatmap(assay(Yeast_rlog)[Yeast_highest20, ], cluster_rows = TRUE, show_rownames = TRUE, cluster_cols = FALSE)
#Creating a heatmap of the lowest 20 expressing genes
Yeast_lowest20 <- order(Yeast_resLFC$baseMean, decreasing = FALSE) [1:20]
pheatmap(assay(Yeast_rlog)[Yeast_lowest20, ], cluster_rows = TRUE, show_rownames = TRUE, cluster_cols = FALSE)
#Installing ReportingTools
BiocManager::install("ReportingTools")'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.3 (2023-03-15
ucrt)
Warning: package(s) not installed when version(s) same as or greater than current;
use `force = TRUE` to re-install: 'ReportingTools'Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.2.3/library
packages:
class, KernSmooth, lattice, MASS, Matrix, nnet, survival
Old packages: 'DelayedArray', 'jsonlite', 'matrixStats'Update all/some/none? [a/s/n]: aWarning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'
There are binary versions available but the source versions are
later:
Binaries will be installedtrying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/DelayedArray_0.23.2.zip'
Content type 'application/zip' length 2449113 bytes (2.3 MB)
downloaded 2.3 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/jsonlite_1.8.4.zip'
Content type 'application/zip' length 1105005 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/matrixStats_1.0.0.zip'
Content type 'application/zip' length 528199 bytes (515 KB)
downloaded 515 KBpackage 'DelayedArray' successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package 'DelayedArray'Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\DelayedArray\libs\x64\DelayedArray.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\DelayedArray\libs\x64\DelayedArray.dll: Permission deniedWarning: restored 'DelayedArray'package 'jsonlite' successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package 'jsonlite'Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\jsonlite\libs\x64\jsonlite.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\jsonlite\libs\x64\jsonlite.dll: Permission deniedWarning: restored 'jsonlite'package 'matrixStats' successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package 'matrixStats'Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\matrixStats\libs\x64\matrixStats.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\matrixStats\libs\x64\matrixStats.dll: Permission deniedWarning: restored 'matrixStats'
The downloaded binary packages are in
C:\Users\benfu\AppData\Local\Temp\RtmpEVmFo6\downloaded_packages#Loading ReportingTools
library(ReportingTools)Loading required package: knitr#Creating a HTML report of output
des2Report <- HTMLReport(shortName = 'Yeast_report', title = 'Yeast RNAseq Analysis', reportDirectory = ".")
publish(YeastDDS_DE, des2Report, factor = YeastDDS_DE$condition)
finish(des2Report)[1] "./Yeast_report.html"#Installing regionReport
BiocManager::install("regionReport")'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.3 (2023-03-15
ucrt)
Warning: package(s) not installed when version(s) same as or greater than current;
use `force = TRUE` to re-install: 'regionReport'Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.2.3/library
packages:
class, KernSmooth, lattice, MASS, Matrix, nnet, survival
Old packages: 'DelayedArray', 'jsonlite', 'matrixStats'Update all/some/none? [a/s/n]: aWarning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'
There are binary versions available but the source versions are
later:
Binaries will be installedtrying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/DelayedArray_0.23.2.zip'
Content type 'application/zip' length 2449113 bytes (2.3 MB)
downloaded 2.3 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/jsonlite_1.8.4.zip'
Content type 'application/zip' length 1105005 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/matrixStats_1.0.0.zip'
Content type 'application/zip' length 528199 bytes (515 KB)
downloaded 515 KBpackage 'DelayedArray' successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package 'DelayedArray'Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\DelayedArray\libs\x64\DelayedArray.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\DelayedArray\libs\x64\DelayedArray.dll: Permission deniedWarning: restored 'DelayedArray'package 'jsonlite' successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package 'jsonlite'Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\jsonlite\libs\x64\jsonlite.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\jsonlite\libs\x64\jsonlite.dll: Permission deniedWarning: restored 'jsonlite'package 'matrixStats' successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package 'matrixStats'Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\matrixStats\libs\x64\matrixStats.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\matrixStats\libs\x64\matrixStats.dll: Permission deniedWarning: restored 'matrixStats'
The downloaded binary packages are in
C:\Users\benfu\AppData\Local\Temp\RtmpEVmFo6\downloaded_packages#Loading regionReport
library(regionReport)#Installing ggplot2
BiocManager::install("ggplot2")'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.3 (2023-03-15
ucrt)
Warning: package(s) not installed when version(s) same as or greater than current;
use `force = TRUE` to re-install: 'ggplot2'Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.2.3/library
packages:
class, KernSmooth, lattice, MASS, Matrix, nnet, survival
Old packages: 'DelayedArray', 'jsonlite', 'matrixStats'Update all/some/none? [a/s/n]: aWarning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'
There are binary versions available but the source versions are
later:
Binaries will be installedtrying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/DelayedArray_0.23.2.zip'
Content type 'application/zip' length 2449113 bytes (2.3 MB)
downloaded 2.3 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/jsonlite_1.8.4.zip'
Content type 'application/zip' length 1105005 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/matrixStats_1.0.0.zip'
Content type 'application/zip' length 528199 bytes (515 KB)
downloaded 515 KBpackage 'DelayedArray' successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package 'DelayedArray'Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\DelayedArray\libs\x64\DelayedArray.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\DelayedArray\libs\x64\DelayedArray.dll: Permission deniedWarning: restored 'DelayedArray'package 'jsonlite' successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package 'jsonlite'Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\jsonlite\libs\x64\jsonlite.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\jsonlite\libs\x64\jsonlite.dll: Permission deniedWarning: restored 'jsonlite'package 'matrixStats' successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package 'matrixStats'Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\matrixStats\libs\x64\matrixStats.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\matrixStats\libs\x64\matrixStats.dll: Permission deniedWarning: restored 'matrixStats'
The downloaded binary packages are in
C:\Users\benfu\AppData\Local\Temp\RtmpEVmFo6\downloaded_packages#Loading ggplot2
library(ggplot2)#Installing DT and sessioninfo
BiocManager::install(c("DT", "sessioninfo"))'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.3 (2023-03-15
ucrt)
Warning: package(s) not installed when version(s) same as or greater than current;
use `force = TRUE` to re-install: 'DT' 'sessioninfo'Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.2.3/library
packages:
class, KernSmooth, lattice, MASS, Matrix, nnet, survival
Old packages: 'DelayedArray', 'jsonlite', 'matrixStats'Update all/some/none? [a/s/n]: aWarning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/data/experiment/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 229Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.16/workflows/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 6873Warning: cannot open URL 'https://bioconductor.org/packages/3.16/books/bin/windows/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'
There are binary versions available but the source versions are
later:
Binaries will be installedtrying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/DelayedArray_0.23.2.zip'
Content type 'application/zip' length 2449113 bytes (2.3 MB)
downloaded 2.3 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/jsonlite_1.8.4.zip'
Content type 'application/zip' length 1105005 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/matrixStats_1.0.0.zip'
Content type 'application/zip' length 528199 bytes (515 KB)
downloaded 515 KBpackage 'DelayedArray' successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package 'DelayedArray'Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\DelayedArray\libs\x64\DelayedArray.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\DelayedArray\libs\x64\DelayedArray.dll: Permission deniedWarning: restored 'DelayedArray'package 'jsonlite' successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package 'jsonlite'Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\jsonlite\libs\x64\jsonlite.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\jsonlite\libs\x64\jsonlite.dll: Permission deniedWarning: restored 'jsonlite'package 'matrixStats' successfully unpacked and MD5 sums checkedWarning: cannot remove prior installation of package 'matrixStats'Warning: problem copying C:\Users\benfu\AppData\Local\R\win-library\4.2\00LOCK\matrixStats\libs\x64\matrixStats.dll to C:\Users\benfu\AppData\Local\R\win-library\4.2\matrixStats\libs\x64\matrixStats.dll: Permission deniedWarning: restored 'matrixStats'
The downloaded binary packages are in
C:\Users\benfu\AppData\Local\Temp\RtmpEVmFo6\downloaded_packages#Loading DT and sessioninfo
library(DT)
library(sessioninfo)#Final Report
DESeq2Report(YeastDDS_DE, project = "Yeast_report_2", intgroup = "condition", colors = NULL, res = NULL, nBest = 200, nBestFeatures = 10, customCode = NULL, outdir = ".", output = "Yeast_report_2", browse = TRUE, device = "png", template = NULL, searchURL = "http://www.ncbi.nlm.nih.gov/gene/?term=", digits = 2)Writing 9 Bibtex entries ... OK
Results written to file './Yeast_report_2.bib'
processing file: Yeast_report_2.Rmd
|
| | 0%
|
|. | 2%
|
|.. | 4% [docSetup]
|
|... | 6%
|
|.... | 9% [setup]
|
|..... | 11%
|
|...... | 13% [PCA]
|
|....... | 15%
|
|....... | 17% [sampleDist]
|
|........ | 19%
|
|......... | 21% [MAplotalpha]
|
|.......... | 23%
|
|........... | 26% [MAplotalphaHalf]
|
|............ | 28%
|
|............. | 30% [MAplotalpha-nBest]
|
|.............. | 32%
|
|............... | 34% [pvalueHistogram]
|
|................ | 36%
|
|................. | 38% [pvalueSumm]
|
|.................. | 40%
|
|................... | 43% [pvalueTable]
|
|.................... | 45%
|
|..................... | 47% [padjHistogram]
|
|...................... | 49%
|
|...................... | 51% [padjSumm]
|
|....................... | 53%
|
|........................ | 55% [padjTable]
|
|......................... | 57%
|
|.......................... | 60% [topFeatures]
|
|........................... | 62%
|
|............................ | 64% [plotCounts]
|
|............................. | 66%
|
|.............................. | 68% [edgeR-BCV]
|
|............................... | 70%
|
|................................ | 72% [edgeR-MDS]
|
|................................. | 74%
|
|.................................. | 77% [unnamed-chunk-13]
|
|................................... | 79%
|
|.................................... | 81% [thecall]
|
|..................................... | 83%
|
|..................................... | 85% [reproducibility1]
|
|...................................... | 87%
|
|....................................... | 89% [reproducibility2]
|
|........................................ | 91%
|
|......................................... | 94% [reproducibility3]
|
|.......................................... | 96%
|
|........................................... | 98% [bibliography]
|
|............................................| 100%
"C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/pandoc" +RTS -K512m -RTS Yeast_report_2.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output Yeast_report_2.html --lua-filter "C:\Users\benfu\AppData\Local\R\win-library\4.2\bookdown\rmarkdown\lua\custom-environment.lua" --lua-filter "C:\Users\benfu\AppData\Local\R\win-library\4.2\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\benfu\AppData\Local\R\win-library\4.2\rmarkdown\rmarkdown\lua\latex-div.lua" --embed-resources --standalone --wrap preserve --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template "C:\Users\benfu\AppData\Local\Temp\RtmpEVmFo6/BiocStyle/template.html" --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --css "C:/Users/benfu/AppData/Local/R/win-library/4.2/BiocStyle/resources/html/bioconductor.css" --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "C:\Users\benfu\AppData\Local\Temp\RtmpEVmFo6\rmarkdown-str5ad884a126f.html" --variable code_folding=hide --variable code_menu=1
[WARNING] This document format requires a nonempty <title> element.
Defaulting to 'Yeast_report_2.knit' as the title.
To specify a title, use 'title' in metadata or --metadata title="...".#Citations for R packages
citation("BiocManager")
To cite package 'BiocManager' in publications use:
Morgan M (2023). _BiocManager: Access the Bioconductor Project
Package Repository_. R package version 1.30.20,
<https://CRAN.R-project.org/package=BiocManager>.
A BibTeX entry for LaTeX users is
@Manual{,
title = {BiocManager: Access the Bioconductor Project Package Repository},
author = {Martin Morgan},
year = {2023},
note = {R package version 1.30.20},
url = {https://CRAN.R-project.org/package=BiocManager},
}citation("Rsubread")
To cite package 'Rsubread' in publications use:
Liao Y, Smyth GK and Shi W (2019). The R package Rsubread is
easier, faster, cheaper and better for alignment and
quantification of RNA sequencing reads. Nucleic Acids Research
47(8), e47.
A BibTeX entry for LaTeX users is
@Article{,
title = {The {R} package {Rsubread} is easier, faster, cheaper and better for alignment and quantification of {RNA} sequencing reads},
author = {Yang Liao and Gordon K. Smyth and Wei Shi},
journal = {Nucleic Acids Research},
year = {2019},
volume = {47},
issue = {8},
pages = {e47},
doi = {10.1093/nar/gkz114},
}citation("DESeq2")
To cite package 'DESeq2' in publications use:
Love, M.I., Huber, W., Anders, S. Moderated estimation of fold
change and dispersion for RNA-seq data with DESeq2 Genome
Biology 15(12):550 (2014)
A BibTeX entry for LaTeX users is
@Article{,
title = {Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
author = {Michael I. Love and Wolfgang Huber and Simon Anders},
year = {2014},
journal = {Genome Biology},
doi = {10.1186/s13059-014-0550-8},
volume = {15},
issue = {12},
pages = {550},
}citation("pheatmap")
To cite package 'pheatmap' in publications use:
Kolde R (2019). _pheatmap: Pretty Heatmaps_. R package version
1.0.12, <https://CRAN.R-project.org/package=pheatmap>.
A BibTeX entry for LaTeX users is
@Manual{,
title = {pheatmap: Pretty Heatmaps},
author = {Raivo Kolde},
year = {2019},
note = {R package version 1.0.12},
url = {https://CRAN.R-project.org/package=pheatmap},
}
ATTENTION: This citation information has been auto-generated from
the package DESCRIPTION file and may need manual editing, see
'help("citation")'.citation("RColorBrewer")
To cite package 'RColorBrewer' in publications use:
Neuwirth E (2022). _RColorBrewer: ColorBrewer Palettes_. R
package version 1.1-3,
<https://CRAN.R-project.org/package=RColorBrewer>.
A BibTeX entry for LaTeX users is
@Manual{,
title = {RColorBrewer: ColorBrewer Palettes},
author = {Erich Neuwirth},
year = {2022},
note = {R package version 1.1-3},
url = {https://CRAN.R-project.org/package=RColorBrewer},
}citation("apeglm")
To cite package 'apeglm' in publications use:
Zhu, A., Ibrahim, J.G., Love, M.I. Heavy-tailed prior
distributions for sequence count data: removing the noise and
preserving large differences Bioinformatics (2018)
A BibTeX entry for LaTeX users is
@Article{,
title = {Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences},
author = {Anqi Zhu and Joseph G. Ibrahim and Michael I. Love},
year = {2018},
journal = {Bioinformatics},
doi = {10.1093/bioinformatics/bty895},
}citation("ComplexHeatmap")
The methods within the code package can be cited as:
Gu, Z. (2016) Complex heatmaps reveal patterns and correlations
in multidimensional genomic data. Bioinformatics.
Gu, Z. (2022) Complex Heatmap Visualization. iMeta.
This free open-source software implements academic research by
the authors and co-workers. If you use it, please support the
project by citing the appropriate journal articles.
To see these entries in BibTeX format, use 'print(<citation>,
bibtex=TRUE)', 'toBibtex(.)', or set
'options(citation.bibtex.max=999)'.citation("ReportingTools")
To cite package 'ReportingTools' in publications use:
Melanie A. Huntley, Jessica L. Larson, Christina Chaivorapol,
Gabriel Becker, Michael Lawrence, Jason A. Hackney, and Joshua
S. Kaminker (in press): ReportingTools: an automated result
processing and presentation toolkit for high throughput genomic
analyses. Bioinformatics
A BibTeX entry for LaTeX users is
@Article{,
title = {ReportingTools: an automated result processing and presentation toolkit for high throughput genomic analyses},
author = {Melanie A. Huntley and Jessica L. Larson and Christina Chaivorapol and Gabriel Becker and Michael Lawrence and Jason A. Hackney and Joshua S. Kaminker},
year = {in press},
journal = {Bioinformatics},
doi = {10.1093/bioinformatics/btt551},
}citation("regionReport")
To cite package 'regionReport' in publications use:
Collado-Torres L, Jaffe AE, Leek JT (2016). "regionReport:
Interactive reports for region-level and feature-level genomic
analyses [version2; referees: 2 approved, 1 approved with
reservations]." _F1000Research_, *4*, 105.
doi:10.12688/f1000research.6379.2
<https://doi.org/10.12688/f1000research.6379.2>,
<http://f1000research.com/articles/4-105/v2>.
Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI,
Langmead B, Irizarry RA, Leek JT, Jaffe AE (2017). "Flexible
expressed region analysis for RNA-seq with derfinder." _Nucl.
Acids Res._. doi:10.1093/nar/gkw852
<https://doi.org/10.1093/nar/gkw852>,
<http://nar.oxfordjournals.org/content/early/2016/09/29/nar.gkw852>.
Collado-Torres L, Jaffe AE, Leek JT (2017). _regionReport:
Generate HTML or PDF reports for a set of genomic regions or
DESeq2/edgeR results_. doi:10.18129/B9.bioc.regionReport
<https://doi.org/10.18129/B9.bioc.regionReport>,
https://github.com/leekgroup/regionReport - R package version
1.32.0, <http://www.bioconductor.org/packages/regionReport>.
To see these entries in BibTeX format, use 'print(<citation>,
bibtex=TRUE)', 'toBibtex(.)', or set
'options(citation.bibtex.max=999)'.citation("ggplot2")
To cite ggplot2 in publications, please use
H. Wickham. ggplot2: Elegant Graphics for Data Analysis.
Springer-Verlag New York, 2016.
A BibTeX entry for LaTeX users is
@Book{,
author = {Hadley Wickham},
title = {ggplot2: Elegant Graphics for Data Analysis},
publisher = {Springer-Verlag New York},
year = {2016},
isbn = {978-3-319-24277-4},
url = {https://ggplot2.tidyverse.org},
}citation("DT")
To cite package 'DT' in publications use:
Xie Y, Cheng J, Tan X (2023). _DT: A Wrapper of the JavaScript
Library 'DataTables'_. R package version 0.28,
<https://CRAN.R-project.org/package=DT>.
A BibTeX entry for LaTeX users is
@Manual{,
title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
author = {Yihui Xie and Joe Cheng and Xianying Tan},
year = {2023},
note = {R package version 0.28},
url = {https://CRAN.R-project.org/package=DT},
}citation("sessioninfo")
To cite package 'sessioninfo' in publications use:
Wickham H, Chang W, Flight R, Müller K, Hester J (2021).
_sessioninfo: R Session Information_. R package version 1.2.2,
<https://CRAN.R-project.org/package=sessioninfo>.
A BibTeX entry for LaTeX users is
@Manual{,
title = {sessioninfo: R Session Information},
author = {Hadley Wickham and Winston Chang and Robert Flight and Kirill Müller and Jim Hester},
year = {2021},
note = {R package version 1.2.2},
url = {https://CRAN.R-project.org/package=sessioninfo},
}---
title: "Saccharomyces Cerevisiae RNA-seq"
output:
  html_notebook: default
  pdf_document: default
---

#Set working directory
```{r}
setwd("C:/Users/benfu/Documents/BIOL3008")
```

#Install BiocManager
```{r}
install.packages("BiocManager")
```

#Checking for updates
```{r}
BiocManager::install()
```
#Installing Rsubread
```{r}
BiocManager::install("Rsubread")
```

#Loading Rsubread 
```{r}
library(Rsubread)
```

#Indexing reference genome
```{r}
buildindex(basename = "Yeast", reference = "Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz")
```

##Mapping RNAseq reads to indexed reference genome individually as this computers disc space is limited. Unable to have all SRR*.fastq files in the directory at the same time.

#SRR20632986
```{r}
align(index = "Yeast", readfile1 = "trimmed_SRR20632986_1.fastq", readfile2 = "trimmed_SRR20632986_2.fastq", type = "rna", input_format = "FASTQ", output_format = "BAM", output_file = "SRR20632986.bam", useAnnotation = TRUE, annot.ext = "Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz", isGTF = TRUE, GTF.featureType = "exon", GTF.attrType = "exon_id")
```

#SRR20632987
```{r}
align(index = "Yeast", readfile1 = "trimmed_SRR20632987_1.fastq", readfile2 = "trimmed_SRR20632987_2.fastq", type = "rna", input_format = "FASTQ", output_format = "BAM", output_file = "SRR20632987.bam", useAnnotation = TRUE, annot.ext = "Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz", isGTF = TRUE, GTF.featureType = "exon", GTF.attrType = "exon_id")
```

#SRR20632988
```{r}
align(index = "Yeast", readfile1 = "trimmed_SRR20632988_1.fastq", readfile2 = "trimmed_SRR20632988_2.fastq", type = "rna", input_format = "FASTQ", output_format = "BAM", output_file = "SRR20632988.bam", useAnnotation = TRUE, annot.ext = "Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz", isGTF = TRUE, GTF.featureType = "exon", GTF.attrType = "exon_id")
```

#SRR20632989
```{r}
align(index = "Yeast", readfile1 = "trimmed_SRR20632989_1.fastq", readfile2 = "trimmed_SRR20632989_2.fastq", type = "rna", input_format = "FASTQ", output_format = "BAM", output_file = "SRR20632989.bam", useAnnotation = TRUE, annot.ext = "Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz", isGTF = TRUE, GTF.featureType = "exon", GTF.attrType = "exon_id")
```

#SRR20632990
```{r}
align(index = "Yeast", readfile1 = "trimmed_SRR20632990_1.fastq", readfile2 = "trimmed_SRR20632990_2.fastq", type = "rna", input_format = "FASTQ", output_format = "BAM", output_file = "SRR20632990.bam", useAnnotation = TRUE, annot.ext = "Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz", isGTF = TRUE, GTF.featureType = "exon", GTF.attrType = "exon_id")
```

#SRR20632991
```{r}
align(index = "Yeast", readfile1 = "trimmed_SRR20632991_1.fastq", readfile2 = "trimmed_SRR20632991_2.fastq", type = "rna", input_format = "FASTQ", output_format = "BAM", output_file = "SRR20632991.bam", useAnnotation = TRUE, annot.ext = "Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz", isGTF = TRUE, GTF.featureType = "exon", GTF.attrType = "exon_id")
```

##Read counts on a single sample
```{r}
SRR20632986_counts <- featureCounts(files = "SRR20632986.bam", annot.ext = "Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz", isGTFAnnotationFile = TRUE, GTF.featureType = "exon", GTF.attrType = "exon_id", useMetaFeatures = TRUE, countMultiMappingReads = TRUE, juncCounts = TRUE, genome = "Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz", isPairedEnd = TRUE, requireBothEndsMapped = TRUE, checkFragLength = TRUE, countChimericFragments = TRUE)
```

#Checking counts file
```{r}
names(SRR20632986_counts)
SRR20632986_counts$targets
SRR20632986_counts$stat
dim(SRR20632986_counts$counts)
head(SRR20632986_counts$counts)
head(SRR20632986_counts$annotation, n=20L)
```

##Feature counts on multiple samples at once (loaded all mapped bam files into directory to complete)
#create a value to address all bam files at once
```{r}
 bams <- list.files(pattern = ".bam$")
```

#Check all of the correct bam files are included and in order
```{r}
head(bams, n=10L)
```

#Running read counts on all samples at once
```{r}
Yeast_counts <- featureCounts(files = bams, annot.ext = "Saccharomyces_cerevisiae.R64-1-1.56.gff3.gz", isGTFAnnotationFile = TRUE, GTF.featureType = "exon", GTF.attrType = "exon_id", useMetaFeatures = TRUE, countMultiMappingReads = TRUE, juncCounts = TRUE, genome = "Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz", isPairedEnd = TRUE, requireBothEndsMapped = TRUE, checkFragLength = TRUE, countChimericFragments = TRUE)
```

#Checking multiple read counts output
```{r}
names(Yeast_counts)
dim(Yeast_counts$counts)
head(Yeast_counts$counts)
head(Yeast_counts$annotation)
tail(Yeast_counts$annotation)
```

##Differential expression with DESeq2
#Create a comma separated value (.csv) file in excel with sample bam files in the same order as the collective bam file created earlier and list WT or mct1 as required
```{r}
YeastSamples <- read.csv("yeast_samples.csv", row.names = 1)
```

#Create a counts matrix
```{r}
Yeast_counts_matrix <- as.matrix(Yeast_counts$counts)
```

#Install DESeq2
```{r}
BiocManager::install("DESeq2")
```

#Load DESeq2
```{r}
library(DESeq2)
```

#Converting the counts matrix into a DESeq2 Data Set 
```{r}
Yeast_dds <- DESeqDataSetFromMatrix(countData = Yeast_counts_matrix, colData = YeastSamples, design = ~ condition)
```
#Retrieved  this error: Error in SummarizedExperiment(assays = SimpleList(counts = countData),  : the rownames and colnames of the supplied assay(s) must be NULL or identical to those of the SummarizedExperiment object (or derivative) to construct
#Error was fixed by correcting the csv file SRR20632** -> SRR206329** (all SRR file names were missing a 9)

#Check Yeast_dds file
```{r}
Yeast_dds
```

#Set the condition for all other conditions to be compared to
```{r}
Yeast_dds$condition <- relevel(Yeast_dds$condition, ref = "WT")
```

#Remove data of genes that with no expression (0), (i.e. "keep" all rows with values above 1)
```{r}
keep <- rowSums(counts(Yeast_dds)) >1
Yeast_dds <- Yeast_dds[keep,]
```

#Check to see if any rows were removed (7507 -> 6921 rows is a 586 reduction, i.e. 586 genes with no expression)
```{r}
dim(Yeast_dds)
```

#Create the rlog normalisation for the samples
```{r}
Yeast_rlog <- rlog(Yeast_dds, blind = TRUE)
```

#Plot result
```{r}
plot(assay(Yeast_rlog) [,1:2], pch=16, cex=0.3)
plot(assay(Yeast_rlog) [,3:4], pch=16, cex=0.3)
plot(assay(Yeast_rlog) [,5:6], pch=16, cex=0.3)
```
#Installing heatmap generation tools
```{r}
BiocManager::install("pheatmap")
BiocManager::install("RcolorBrewer")
```

#Loading heatmap tools
```{r}
library(pheatmap)
library(RColorBrewer)
```

#Creating the distance matrix
```{r}
Yeast_sampleDist <- dist(t(assay(Yeast_rlog)))
Yeast_sampleDist
```

#Heatmap of sample distances
```{r}
Yeast_sampleDistMatrix <- as.matrix(Yeast_sampleDist)
row.names(Yeast_sampleDistMatrix) <- paste(Yeast_rlog$condition, Yeast_rlog$sizeFactor, sep = "-")
colnames(Yeast_sampleDistMatrix) <- NULL
colours <- colorRampPalette(rev(brewer.pal(9, "Blues")))(255)
pheatmap(Yeast_sampleDistMatrix, clustering_distance_rows = Yeast_sampleDist, clustering_distance_cols = Yeast_sampleDist, color = colours)
```

#Creating a Principal components analysis (PCA) plot
```{r}
plotPCA(Yeast_rlog)
```

#Calculating differentially expressed genes
```{r}
YeastDDS_DE <- DESeq(Yeast_dds)
Yeast_res <- results(YeastDDS_DE)
Yeast_res
mcols(Yeast_res, use.names = TRUE)
```

#Examining the results 
```{r}
summary(Yeast_res)
```

#Finding the number of adjusted p-values < 0.1 
```{r}
sum(Yeast_res$padj < 0.1, na.rm = TRUE)
```

#Changing the adjusted p-value cutoff to 0.05 (reset false discovery rate)
```{r}
Yeast_res_5 <- results(YeastDDS_DE, alpha = 0.05)
table(Yeast_res_5$padj < 0.05)
```

#Examine results with reduced adjusted p-value cutoff
```{r}
summary(Yeast_res_5)
```

#Ordering results table by smallest p-value and adjusted p-value, respectively 
```{r}
Yeast_res_ordered <- Yeast_res[order(Yeast_res$pvalue),]
Yeast_res_ordpadj <- Yeast_res[order(Yeast_res$padj),]
```

##Viewing and comparing results, ordered results (p-value) and ordered results (adjusted p-value) #Heads
```{r}
head(Yeast_res)
head(Yeast_res_ordered)
head(Yeast_res_ordpadj)
```
#Tails
```{r}
tail(Yeast_res)
tail(Yeast_res_ordered)
tail(Yeast_res_ordpadj)
```

#Visualisation of differentially expressed genes with an MA plot
```{r}
plotMA(Yeast_res, ylim=c(-5,5))
```
#Checking the names in the differential expression file
```{r}
resultsNames(YeastDDS_DE)
```

#Installing apeglm package
```{r}
BiocManager::install("apeglm")
```

#Load apeglm
```{r}
library(apeglm)
```

#Creating log fold change on the results of differential expression
```{r}
Yeast_resLFC <- lfcShrink(YeastDDS_DE, coef = "condition_mct1_vs_WT", type = "apeglm")
```

#check file
```{r}
Yeast_resLFC
```

#MA plot of log fold change
```{r}
plotMA(Yeast_resLFC, ylim=c(-10,10))
```

#Finding genes with expressions more than doubled or halved the original
```{r}
Yeast_resLFC1 <- results(YeastDDS_DE, lfcThreshold = 1)
```

```{r}
table(Yeast_resLFC1$padj < 0.01)
```

#Finding the highest adjusted p-value where all results are false 
```{r}
table(Yeast_resLFC1$padj < 1E-22)
```

```{r}
table(Yeast_resLFC1$padj < 1E-23)
```

#MA plot of genes with expressions more than doubled or halved the original
```{r}
plotMA(Yeast_resLFC1, ylim=c(-10,10))
```

#Genes with a false discovery rate less than 5%
```{r}
Yeast_res_5sub <- subset(Yeast_res, padj < 0.05)
```

#Head
```{r}
head(Yeast_res_5sub[order(Yeast_res_5sub$log2FoldChange),])
```

#MA plot of the genes with a false discovery rate less than 5%
```{r}
plotMA(Yeast_res_5sub, ylim=c(-10,10))
```

#MA plot of all the genes
```{r}
plotMA(Yeast_res, ylim=c(-10,10))
```

#Visualisation of the counts for the gene with the smallest adjusted p-value 
```{r}
plotCounts(Yeast_dds, gene = which.min(Yeast_res$padj), intgroup = "condition")
```

#Visualisation of the counts for the gene with the largest adjusted p-value
```{r}
plotCounts(Yeast_dds, gene = which.max(Yeast_res$padj), intgroup = "condition")
```

#Visualisation of the counts for the YAL067W-A_mRNA-E1 gene
```{r}
plotCounts(Yeast_dds, "YAL067W-A_mRNA-E1", intgroup = "condition", xlab = "Group")
```

#Visualisation of the counts for the YOR221C_mRNA-E1 gene
```{r}
plotCounts(Yeast_dds, "YOR221C_mRNA-E1", intgroup = "condition", xlab = "Group")
```

#Installing ComplexHeatmap tool
```{r}
BiocManager::install("ComplexHeatmap")
```

#Loading ComplexHeatmap
```{r}
library(ComplexHeatmap)
```

#Creating a heatmap of the highest 20 log2fold change genes
```{r}
Yeast_top20 <- order(Yeast_resLFC$log2FoldChange, decreasing = TRUE) [1:20]
pheatmap(assay(Yeast_rlog)[Yeast_top20, ], cluster_rows = TRUE, show_rownames = TRUE, cluster_cols = FALSE)
```

#Creating a heatmap of the lowest 20 log2fold change genes
```{r}
Yeast_bottom20 <- order(Yeast_resLFC$log2FoldChange, decreasing = FALSE) [1:20]
pheatmap(assay(Yeast_rlog)[Yeast_bottom20, ], cluster_rows = TRUE, show_rownames = TRUE, cluster_cols = FALSE)
```

#Creating a heatmap of the highest 20 expressing genes
```{r}
Yeast_highest20 <- order(Yeast_resLFC$baseMean, decreasing = TRUE) [1:20]
pheatmap(assay(Yeast_rlog)[Yeast_highest20, ], cluster_rows = TRUE, show_rownames = TRUE, cluster_cols = FALSE)
```

#Creating a heatmap of the lowest 20 expressing genes
```{r}
Yeast_lowest20 <- order(Yeast_resLFC$baseMean, decreasing = FALSE) [1:20]
pheatmap(assay(Yeast_rlog)[Yeast_lowest20, ], cluster_rows = TRUE, show_rownames = TRUE, cluster_cols = FALSE)
```

#Installing ReportingTools
```{r}
BiocManager::install("ReportingTools")
```

#Loading ReportingTools
```{r}
library(ReportingTools)
```

#Creating a HTML report of output
```{r}
des2Report <- HTMLReport(shortName = 'Yeast_report', title = 'Yeast RNAseq Analysis', reportDirectory = ".")
publish(YeastDDS_DE, des2Report, factor = YeastDDS_DE$condition)
finish(des2Report)
```

#Installing regionReport
```{r}
BiocManager::install("regionReport")
```

#Loading regionReport
```{r}
library(regionReport)
```

#Installing ggplot2
```{r}
BiocManager::install("ggplot2")
```

#Loading ggplot2
```{r}
library(ggplot2)
```

#Installing DT and sessioninfo
```{r}
BiocManager::install(c("DT", "sessioninfo"))
```

#Loading DT and sessioninfo
```{r}
library(DT)
library(sessioninfo)
```

#Final Report
```{r}
DESeq2Report(YeastDDS_DE, project = "Yeast_report_2", intgroup = "condition", colors = NULL, res = NULL, nBest = 200, nBestFeatures = 10, customCode = NULL, outdir = ".", output = "Yeast_report_2", browse = TRUE, device = "png", template = NULL, searchURL = "http://www.ncbi.nlm.nih.gov/gene/?term=", digits = 2)
```

#Citations for R packages
```{r}
citation("BiocManager")
citation("Rsubread")
citation("DESeq2")
citation("pheatmap")
citation("RColorBrewer")
citation("apeglm")
citation("ComplexHeatmap")
citation("ReportingTools")
citation("regionReport")
citation("ggplot2")
citation("DT")
citation("sessioninfo")
```
