#install library
#devtools::install_github("ipatop/shRNAtools")
library(shRNAtools)This package contains two functions that will generate a Data Frame or tab separated file with the original table plus the shRNA Oligo design appended.
The input should be a tab separated table with circRNA or linear RNA splicing junction coordinates and gene names in the format:
| Name | Chr | Start | End | Strand |
|---|---|---|---|---|
| circMbl | chr2R | 17275410 | 17276063 | + |
This table can have an optional column with the Strand
So far the following species are available:
Input should look like this
#Copy and paste the full path of the test data into the readtable argument
system.file("extdata", "circs_totest.txt", package = "shRNAtools")
#> [1] "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/shRNAtools/extdata/circs_totest.txt"
read.table(file = "/Users/inespatop/Documents/shRNA_design_circRNA/shRNAtools/inst/extdata/circs_totest.txt",header = T)
#> dm6 circ_name SYMBOL Chr
#> 1 chr2R:17275410-17276063 mbl_chr2R:17275410-17276063 mbl chr2R
#> 2 chr3L:24725824-24726292 scro_chr3L:24725824-24726292 scro chr3L
#> 3 chr2R:5423750-5424239 stw_chr2R:5423750-5424239 stw chr2R
#> 4 chr3R:4626973-4628349 5-HT2A_chr3R:4626973-4628349 5-HT2A chr3R
#> 5 chr3L:12851309-12852277 Wbp2_chr3L:12851309-12852277 Wbp2 chr3L
#> 6 chr2R:15735091-15737060 CG30089_chr2R:15735091-15737060 CG30089 chr2R
#> 7 chr3R:14529177-14530230 Pde6_chr3R:14529177-14530230 Pde6 chr3R
#> Start End Strand
#> 1 17275410 17276063 +
#> 2 24725824 24726292 +
#> 3 5423750 5424239 +
#> 4 4626973 4628349 +
#> 5 12851309 12852277 +
#> 6 15735091 15737060 +
#> 7 14529177 14530230 -Run to create an output table
#Copy and paste the full path of the test data into the readtable argument
system.file("extdata", "circs_totest.txt", package = "shRNAtools")
#> [1] "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/shRNAtools/extdata/circs_totest.txt"
circRNASpliceOligoDesigner(input_coordinates = "../test/circs_totest.txt",output = "../test/New_out.tsv")
#> Loading required package: TxDb.Dmelanogaster.UCSC.dm6.ensGene
#> Loading required package: GenomicFeatures
#> 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, 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
#> Loading required package: S4Vectors
#> Loading required package: stats4
#>
#> Attaching package: 'S4Vectors'
#> The following objects are masked from 'package:base':
#>
#> expand.grid, I, unname
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: GenomicRanges
#> Loading required package: AnnotationDbi
#> 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")'.
#> Loading required package: BSgenome.Dmelanogaster.UCSC.dm6
#> Loading required package: BSgenome
#> Loading required package: Biostrings
#> Loading required package: XVector
#>
#> Attaching package: 'Biostrings'
#> The following object is masked from 'package:base':
#>
#> strsplit
#> Loading required package: rtracklayerRun to create a DataFrame, if writetab = F
circOligos<-circRNASpliceOligoDesigner(input_coordinates = "../test/circs_totest.txt",output = "../test/New_out.tsv",writetab = F)Output
circOligos
#> dm6 circ_name SYMBOL Chr
#> 1 chr2R:17275410-17276063 mbl_chr2R:17275410-17276063 mbl chr2R
#> 2 chr3L:24725824-24726292 scro_chr3L:24725824-24726292 scro chr3L
#> 3 chr2R:5423750-5424239 NA_chr2R:5423750-5424239 <NA> chr2R
#> 4 chr3R:4626973-4628349 5-HT2A_chr3R:4626973-4628349 5-HT2A chr3R
#> 5 chr3L:12851309-12852277 Wbp2_chr3L:12851309-12852277 Wbp2 chr3L
#> 6 chr2R:15735091-15737060 CG30089_chr2R:15735091-15737060 CG30089 chr2R
#> 7 chr3R:14529177-14530230 Pde6_chr3R:14529177-14530230 Pde6 chr3R
#> Start End junction_long
#> 1 17275410 17276063 GCCTGCTACGACAGCATCAAGATAATGTAAACTCAGCTTACA
#> 2 24725824 24726292 AAATCCACCATCTCCGTTTCGCGATAAAAGCCTACTACCAAC
#> 3 5423750 5424239 ATACTACACAGTATTGGGAGCAAAATCAACCAGATCTTACAC
#> 4 4626973 4628349 CTATCCAAACCTAATGGACAGGGTATTGGCCACTTGGCTTTA
#> 5 12851309 12852277 CTCAAATAGCCATCCCGACAACACCACCTGCTCACCAACCAG
#> 6 15735091 15737060 GCCGCTGCCCATCATGCGCAGAATTGCGATCCATTCACGCCA
#> 7 14529177 14530230 TTTCCCTTTGATTGAAGAAACCTGCTGCACGGTGGGCGATGC
#> junction junction_revcomp
#> 1 CAGCATCAAGATAATGTAAAC GTTTACATTATCTTGATGCTG
#> 2 CTCCGTTTCGCGATAAAAGCC GGCTTTTATCGCGAAACGGAG
#> 3 TATTGGGAGCAAAATCAACCA TGGTTGATTTTGCTCCCAATA
#> 4 TAATGGACAGGGTATTGGCCA TGGCCAATACCCTGTCCATTA
#> 5 ATCCCGACAACACCACCTGCT AGCAGGTGGTGTTGTCGGGAT
#> 6 TCATGCGCAGAATTGCGATCC GGATCGCAATTCTGCGCATGA
#> 7 TTGAAGAAACCTGCTGCACGG CCGTGCAGCAGGTTTCTTCAA
#> TopStrand
#> 1 ctagcagtCAGCATCAAGATAATGTAAACtagttatattcaagcataGTTTACATTATCTTGATGCTGgcg
#> 2 ctagcagtCTCCGTTTCGCGATAAAAGCCtagttatattcaagcataGGCTTTTATCGCGAAACGGAGgcg
#> 3 ctagcagtTATTGGGAGCAAAATCAACCAtagttatattcaagcataTGGTTGATTTTGCTCCCAATAgcg
#> 4 ctagcagtTAATGGACAGGGTATTGGCCAtagttatattcaagcataTGGCCAATACCCTGTCCATTAgcg
#> 5 ctagcagtATCCCGACAACACCACCTGCTtagttatattcaagcataAGCAGGTGGTGTTGTCGGGATgcg
#> 6 ctagcagtTCATGCGCAGAATTGCGATCCtagttatattcaagcataGGATCGCAATTCTGCGCATGAgcg
#> 7 ctagcagtTTGAAGAAACCTGCTGCACGGtagttatattcaagcataCCGTGCAGCAGGTTTCTTCAAgcg
#> BotStrand
#> 1 aattcgcCAGCATCAAGATAATGTAAACtatgcttgaatataactaGTTTACATTATCTTGATGCTGactg
#> 2 aattcgcCTCCGTTTCGCGATAAAAGCCtatgcttgaatataactaGGCTTTTATCGCGAAACGGAGactg
#> 3 aattcgcTATTGGGAGCAAAATCAACCAtatgcttgaatataactaTGGTTGATTTTGCTCCCAATAactg
#> 4 aattcgcTAATGGACAGGGTATTGGCCAtatgcttgaatataactaTGGCCAATACCCTGTCCATTAactg
#> 5 aattcgcATCCCGACAACACCACCTGCTtatgcttgaatataactaAGCAGGTGGTGTTGTCGGGATactg
#> 6 aattcgcTCATGCGCAGAATTGCGATCCtatgcttgaatataactaGGATCGCAATTCTGCGCATGAactg
#> 7 aattcgcTTGAAGAAACCTGCTGCACGGtatgcttgaatataactaCCGTGCAGCAGGTTTCTTCAAactg
#> junction5p junction_revcomp5p
#> 1 CATCAAGATAATGTAAACTCA TGAGTTTACATTATCTTGATG
#> 2 CGTTTCGCGATAAAAGCCTAC GTAGGCTTTTATCGCGAAACG
#> 3 TGGGAGCAAAATCAACCAGAT ATCTGGTTGATTTTGCTCCCA
#> 4 TGGACAGGGTATTGGCCACTT AAGTGGCCAATACCCTGTCCA
#> 5 CCGACAACACCACCTGCTCAC GTGAGCAGGTGGTGTTGTCGG
#> 6 TGCGCAGAATTGCGATCCATT AATGGATCGCAATTCTGCGCA
#> 7 AAGAAACCTGCTGCACGGTGG CCACCGTGCAGCAGGTTTCTT
#> TopStrand5p
#> 1 ctagcagtCATCAAGATAATGTAAACTCAtagttatattcaagcataTGAGTTTACATTATCTTGATGgcg
#> 2 ctagcagtCGTTTCGCGATAAAAGCCTACtagttatattcaagcataGTAGGCTTTTATCGCGAAACGgcg
#> 3 ctagcagtTGGGAGCAAAATCAACCAGATtagttatattcaagcataATCTGGTTGATTTTGCTCCCAgcg
#> 4 ctagcagtTGGACAGGGTATTGGCCACTTtagttatattcaagcataAAGTGGCCAATACCCTGTCCAgcg
#> 5 ctagcagtCCGACAACACCACCTGCTCACtagttatattcaagcataGTGAGCAGGTGGTGTTGTCGGgcg
#> 6 ctagcagtTGCGCAGAATTGCGATCCATTtagttatattcaagcataAATGGATCGCAATTCTGCGCAgcg
#> 7 ctagcagtAAGAAACCTGCTGCACGGTGGtagttatattcaagcataCCACCGTGCAGCAGGTTTCTTgcg
#> BotStrand5p
#> 1 aattcgcCATCAAGATAATGTAAACTCAtatgcttgaatataactaTGAGTTTACATTATCTTGATGactg
#> 2 aattcgcCGTTTCGCGATAAAAGCCTACtatgcttgaatataactaGTAGGCTTTTATCGCGAAACGactg
#> 3 aattcgcTGGGAGCAAAATCAACCAGATtatgcttgaatataactaATCTGGTTGATTTTGCTCCCAactg
#> 4 aattcgcTGGACAGGGTATTGGCCACTTtatgcttgaatataactaAAGTGGCCAATACCCTGTCCAactg
#> 5 aattcgcCCGACAACACCACCTGCTCACtatgcttgaatataactaGTGAGCAGGTGGTGTTGTCGGactg
#> 6 aattcgcTGCGCAGAATTGCGATCCATTtatgcttgaatataactaAATGGATCGCAATTCTGCGCAactg
#> 7 aattcgcAAGAAACCTGCTGCACGGTGGtatgcttgaatataactaCCACCGTGCAGCAGGTTTCTTactg
#> junction3p junction_revcomp3p
#> 1 GACAGCATCAAGATAATGTAA TTACATTATCTTGATGCTGTC
#> 2 ATCTCCGTTTCGCGATAAAAG CTTTTATCGCGAAACGGAGAT
#> 3 AGTATTGGGAGCAAAATCAAC GTTGATTTTGCTCCCAATACT
#> 4 CCTAATGGACAGGGTATTGGC GCCAATACCCTGTCCATTAGG
#> 5 CCATCCCGACAACACCACCTG CAGGTGGTGTTGTCGGGATGG
#> 6 CATCATGCGCAGAATTGCGAT ATCGCAATTCTGCGCATGATG
#> 7 GATTGAAGAAACCTGCTGCAC GTGCAGCAGGTTTCTTCAATC
#> TopStrand3p
#> 1 ctagcagtGACAGCATCAAGATAATGTAAtagttatattcaagcataTTACATTATCTTGATGCTGTCgcg
#> 2 ctagcagtATCTCCGTTTCGCGATAAAAGtagttatattcaagcataCTTTTATCGCGAAACGGAGATgcg
#> 3 ctagcagtAGTATTGGGAGCAAAATCAACtagttatattcaagcataGTTGATTTTGCTCCCAATACTgcg
#> 4 ctagcagtCCTAATGGACAGGGTATTGGCtagttatattcaagcataGCCAATACCCTGTCCATTAGGgcg
#> 5 ctagcagtCCATCCCGACAACACCACCTGtagttatattcaagcataCAGGTGGTGTTGTCGGGATGGgcg
#> 6 ctagcagtCATCATGCGCAGAATTGCGATtagttatattcaagcataATCGCAATTCTGCGCATGATGgcg
#> 7 ctagcagtGATTGAAGAAACCTGCTGCACtagttatattcaagcataGTGCAGCAGGTTTCTTCAATCgcg
#> BotStrand3p
#> 1 aattcgcGACAGCATCAAGATAATGTAAtatgcttgaatataactaTTACATTATCTTGATGCTGTCactg
#> 2 aattcgcATCTCCGTTTCGCGATAAAAGtatgcttgaatataactaCTTTTATCGCGAAACGGAGATactg
#> 3 aattcgcAGTATTGGGAGCAAAATCAACtatgcttgaatataactaGTTGATTTTGCTCCCAATACTactg
#> 4 aattcgcCCTAATGGACAGGGTATTGGCtatgcttgaatataactaGCCAATACCCTGTCCATTAGGactg
#> 5 aattcgcCCATCCCGACAACACCACCTGtatgcttgaatataactaCAGGTGGTGTTGTCGGGATGGactg
#> 6 aattcgcCATCATGCGCAGAATTGCGATtatgcttgaatataactaATCGCAATTCTGCGCATGATGactg
#> 7 aattcgcGATTGAAGAAACCTGCTGCACtatgcttgaatataactaGTGCAGCAGGTTTCTTCAATCactgInput should look like this
#Copy and paste the full path of the test data into the readtable argument
system.file("extdata", "lin_totest.txt", package = "shRNAtools")
#> [1] "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/shRNAtools/extdata/lin_totest.txt"
read.table(file = "/Users/inespatop/Documents/shRNA_design_circRNA/shRNAtools/inst/extdata/lin_totest.txt",header = T)
#> Warning in read.table(file =
#> "/Users/inespatop/Documents/shRNA_design_circRNA/shRNAtools/inst/extdata/lin_totest.txt", :
#> incomplete final line found by readTableHeader on
#> '/Users/inespatop/Documents/shRNA_design_circRNA/shRNAtools/inst/extdata/lin_totest.txt'
#> dm6 SYMBOL Chr Start End Strand
#> 1 chr2R:17362078-17373067 mblC chr2R 17362078 17373067 +
#> 2 chr2R:17371151-17373071 mblOP1 chr2R 17371151 17373071 +
#> 3 chr2R:17373161-17373816 mblOP2 chr2R 17373161 17373816 +Run to create an output table
#Copy and paste the full path of the test data into the readtable argument
system.file("extdata", "lin_totest.txt", package = "shRNAtools")
#> [1] "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/shRNAtools/extdata/lin_totest.txt"
linRNASpliceOligoDesigner(input_coordinates = "../test/circs_totest.txt",output = "../test/New_out_lin.tsv")Run to create a DataFrame, if writetab = F
linOligos<-linRNASpliceOligoDesigner(input_coordinates = "../test/circs_totest.txt",output = "../test/New_out.tsv",writetab = F)Output
linOligos
#> dm6 circ_name SYMBOL Chr
#> 1 chr2R:17275410-17276063 mbl_chr2R:17275410-17276063 mbl chr2R
#> 2 chr3L:24725824-24726292 scro_chr3L:24725824-24726292 scro chr3L
#> 3 chr2R:5423750-5424239 NA_chr2R:5423750-5424239 <NA> chr2R
#> 4 chr3R:4626973-4628349 5-HT2A_chr3R:4626973-4628349 5-HT2A chr3R
#> 5 chr3L:12851309-12852277 Wbp2_chr3L:12851309-12852277 Wbp2 chr3L
#> 6 chr2R:15735091-15737060 CG30089_chr2R:15735091-15737060 CG30089 chr2R
#> 7 chr3R:14529177-14530230 Pde6_chr3R:14529177-14530230 Pde6 chr3R
#> Start End junction_long
#> 1 17275410 17276063 CTCTTTTACTCTCATTTCAGAGGTCAGTACTCCCATACCCTT
#> 2 24725824 24726292 TTTTTTTTTTTGTATTTTAGCGGTAAATATAAGTAGATCGTT
#> 3 5423750 5424239 ATTTTTTTTATTTTATGCAGACGTAAGTATTCAAAATTCCAA
#> 4 4626973 4628349 CATAGATATTTGTTTTTCAGGGGTAATAGGAAAACACCTGAA
#> 5 12851309 12852277 TCCTCTCTTTTTCGTCTTAGCAGTAAGATTTATTGTTTCAAT
#> 6 15735091 15737060 TTTCCACCTCTCTCCCGCAGAGGTGAGTTCCCACTAGCCCAC
#> 7 14529177 14530230 TTCTTATGTTAAGTAGTTACCCCTGAAAAAAAAGAGCGGAGA
#> junction junction_revcomp
#> 1 TCATTTCAGAGGTCAGTACTC GAGTACTGACCTCTGAAATGA
#> 2 GTATTTTAGCGGTAAATATAA TTATATTTACCGCTAAAATAC
#> 3 TTTATGCAGACGTAAGTATTC GAATACTTACGTCTGCATAAA
#> 4 GTTTTTCAGGGGTAATAGGAA TTCCTATTACCCCTGAAAAAC
#> 5 TCGTCTTAGCAGTAAGATTTA TAAATCTTACTGCTAAGACGA
#> 6 CTCCCGCAGAGGTGAGTTCCC GGGAACTCACCTCTGCGGGAG
#> 7 AGTAGTTACCCCTGAAAAAAA TTTTTTTCAGGGGTAACTACT
#> TopStrand
#> 1 ctagcagtTCATTTCAGAGGTCAGTACTCtagttatattcaagcataGAGTACTGACCTCTGAAATGAgcg
#> 2 ctagcagtGTATTTTAGCGGTAAATATAAtagttatattcaagcataTTATATTTACCGCTAAAATACgcg
#> 3 ctagcagtTTTATGCAGACGTAAGTATTCtagttatattcaagcataGAATACTTACGTCTGCATAAAgcg
#> 4 ctagcagtGTTTTTCAGGGGTAATAGGAAtagttatattcaagcataTTCCTATTACCCCTGAAAAACgcg
#> 5 ctagcagtTCGTCTTAGCAGTAAGATTTAtagttatattcaagcataTAAATCTTACTGCTAAGACGAgcg
#> 6 ctagcagtCTCCCGCAGAGGTGAGTTCCCtagttatattcaagcataGGGAACTCACCTCTGCGGGAGgcg
#> 7 ctagcagtAGTAGTTACCCCTGAAAAAAAtagttatattcaagcataTTTTTTTCAGGGGTAACTACTgcg
#> BotStrand
#> 1 aattcgcTCATTTCAGAGGTCAGTACTCtatgcttgaatataactaGAGTACTGACCTCTGAAATGAactg
#> 2 aattcgcGTATTTTAGCGGTAAATATAAtatgcttgaatataactaTTATATTTACCGCTAAAATACactg
#> 3 aattcgcTTTATGCAGACGTAAGTATTCtatgcttgaatataactaGAATACTTACGTCTGCATAAAactg
#> 4 aattcgcGTTTTTCAGGGGTAATAGGAAtatgcttgaatataactaTTCCTATTACCCCTGAAAAACactg
#> 5 aattcgcTCGTCTTAGCAGTAAGATTTAtatgcttgaatataactaTAAATCTTACTGCTAAGACGAactg
#> 6 aattcgcCTCCCGCAGAGGTGAGTTCCCtatgcttgaatataactaGGGAACTCACCTCTGCGGGAGactg
#> 7 aattcgcAGTAGTTACCCCTGAAAAAAAtatgcttgaatataactaTTTTTTTCAGGGGTAACTACTactg
#> junction5p junction_revcomp5p
#> 1 TTTCAGAGGTCAGTACTCCCA TGGGAGTACTGACCTCTGAAA
#> 2 TTTTAGCGGTAAATATAAGTA TACTTATATTTACCGCTAAAA
#> 3 ATGCAGACGTAAGTATTCAAA TTTGAATACTTACGTCTGCAT
#> 4 TTTCAGGGGTAATAGGAAAAC GTTTTCCTATTACCCCTGAAA
#> 5 TCTTAGCAGTAAGATTTATTG CAATAAATCTTACTGCTAAGA
#> 6 CCGCAGAGGTGAGTTCCCACT AGTGGGAACTCACCTCTGCGG
#> 7 AGTTACCCCTGAAAAAAAAGA TCTTTTTTTTCAGGGGTAACT
#> TopStrand5p
#> 1 ctagcagtTTTCAGAGGTCAGTACTCCCAtagttatattcaagcataTGGGAGTACTGACCTCTGAAAgcg
#> 2 ctagcagtTTTTAGCGGTAAATATAAGTAtagttatattcaagcataTACTTATATTTACCGCTAAAAgcg
#> 3 ctagcagtATGCAGACGTAAGTATTCAAAtagttatattcaagcataTTTGAATACTTACGTCTGCATgcg
#> 4 ctagcagtTTTCAGGGGTAATAGGAAAACtagttatattcaagcataGTTTTCCTATTACCCCTGAAAgcg
#> 5 ctagcagtTCTTAGCAGTAAGATTTATTGtagttatattcaagcataCAATAAATCTTACTGCTAAGAgcg
#> 6 ctagcagtCCGCAGAGGTGAGTTCCCACTtagttatattcaagcataAGTGGGAACTCACCTCTGCGGgcg
#> 7 ctagcagtAGTTACCCCTGAAAAAAAAGAtagttatattcaagcataTCTTTTTTTTCAGGGGTAACTgcg
#> BotStrand5p
#> 1 aattcgcTTTCAGAGGTCAGTACTCCCAtatgcttgaatataactaTGGGAGTACTGACCTCTGAAAactg
#> 2 aattcgcTTTTAGCGGTAAATATAAGTAtatgcttgaatataactaTACTTATATTTACCGCTAAAAactg
#> 3 aattcgcATGCAGACGTAAGTATTCAAAtatgcttgaatataactaTTTGAATACTTACGTCTGCATactg
#> 4 aattcgcTTTCAGGGGTAATAGGAAAACtatgcttgaatataactaGTTTTCCTATTACCCCTGAAAactg
#> 5 aattcgcTCTTAGCAGTAAGATTTATTGtatgcttgaatataactaCAATAAATCTTACTGCTAAGAactg
#> 6 aattcgcCCGCAGAGGTGAGTTCCCACTtatgcttgaatataactaAGTGGGAACTCACCTCTGCGGactg
#> 7 aattcgcAGTTACCCCTGAAAAAAAAGAtatgcttgaatataactaTCTTTTTTTTCAGGGGTAACTactg
#> junction3p junction_revcomp3p
#> 1 TCTCATTTCAGAGGTCAGTAC GTACTGACCTCTGAAATGAGA
#> 2 TTGTATTTTAGCGGTAAATAT ATATTTACCGCTAAAATACAA
#> 3 ATTTTATGCAGACGTAAGTAT ATACTTACGTCTGCATAAAAT
#> 4 TTGTTTTTCAGGGGTAATAGG CCTATTACCCCTGAAAAACAA
#> 5 TTTCGTCTTAGCAGTAAGATT AATCTTACTGCTAAGACGAAA
#> 6 CTCTCCCGCAGAGGTGAGTTC GAACTCACCTCTGCGGGAGAG
#> 7 TAAGTAGTTACCCCTGAAAAA TTTTTCAGGGGTAACTACTTA
#> TopStrand3p
#> 1 ctagcagtTCTCATTTCAGAGGTCAGTACtagttatattcaagcataGTACTGACCTCTGAAATGAGAgcg
#> 2 ctagcagtTTGTATTTTAGCGGTAAATATtagttatattcaagcataATATTTACCGCTAAAATACAAgcg
#> 3 ctagcagtATTTTATGCAGACGTAAGTATtagttatattcaagcataATACTTACGTCTGCATAAAATgcg
#> 4 ctagcagtTTGTTTTTCAGGGGTAATAGGtagttatattcaagcataCCTATTACCCCTGAAAAACAAgcg
#> 5 ctagcagtTTTCGTCTTAGCAGTAAGATTtagttatattcaagcataAATCTTACTGCTAAGACGAAAgcg
#> 6 ctagcagtCTCTCCCGCAGAGGTGAGTTCtagttatattcaagcataGAACTCACCTCTGCGGGAGAGgcg
#> 7 ctagcagtTAAGTAGTTACCCCTGAAAAAtagttatattcaagcataTTTTTCAGGGGTAACTACTTAgcg
#> BotStrand3p
#> 1 aattcgcTCTCATTTCAGAGGTCAGTACtatgcttgaatataactaGTACTGACCTCTGAAATGAGAactg
#> 2 aattcgcTTGTATTTTAGCGGTAAATATtatgcttgaatataactaATATTTACCGCTAAAATACAAactg
#> 3 aattcgcATTTTATGCAGACGTAAGTATtatgcttgaatataactaATACTTACGTCTGCATAAAATactg
#> 4 aattcgcTTGTTTTTCAGGGGTAATAGGtatgcttgaatataactaCCTATTACCCCTGAAAAACAAactg
#> 5 aattcgcTTTCGTCTTAGCAGTAAGATTtatgcttgaatataactaAATCTTACTGCTAAGACGAAAactg
#> 6 aattcgcCTCTCCCGCAGAGGTGAGTTCtatgcttgaatataactaGAACTCACCTCTGCGGGAGAGactg
#> 7 aattcgcTAAGTAGTTACCCCTGAAAAAtatgcttgaatataactaTTTTTCAGGGGTAACTACTTAactgThe following packages are required, here an example of how to install it
install.packages("dplyr")
install.packages("tidyr")
BiocManager::install("Rsubread")
BiocManager::install("GenomicFeatures")
BiocManager::install("Biostrings")
BiocManager::install("TxDb.Dmelanogaster.UCSC.dm6.ensGene")
BiocManager::install("BSgenome.Dmelanogaster.UCSC.dm6")
BiocManager::install("TxDb.Dmelanogaster.UCSC.dm3.ensGene")
BiocManager::install("BSgenome.Dmelanogaster.UCSC.dm3")
BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")
BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene")
BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")
BiocManager::install("TxDb.Mmusculus.UCSC.mm10.knownGene")
BiocManager::install("BSgenome.Mmusculus.UCSC.mm10")
BiocManager::install("TxDb.Rnorvegicus.UCSC.rn4.ensGene")
BiocManager::install("BSgenome.Rnorvegicus.UCSC.rn4")