Ribo-Seq Analysis for GSE62134 RiboProfiling

rr suppressMessages(library(RiboProfiling))

replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboProfiling’

rr suppressMessages(library(GenomicFeatures)) suppressMessages(library(BiocGenerics)) suppressMessages(library(cowplot)) riboFiles <- paste(‘/media/rna/public_Ribo/GSE62134/single_end/mapped/bams/SRR160529’, c(3,4,5,6,7,8,9), sep=‘’) riboFiles <- c(riboFiles,’/media/rna/public_Ribo/GSE62134/single_end/mapped/bams/SRR1605300’) riboFiles <- paste(riboFiles, ‘bam’, sep=‘.’) gtf <- ‘/media/dna/genomes/mm10/annotation/gencode.vM11.annotation.gtf’ TxDb <- makeTxDbFromGFF(gtf)

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... RSQLite::dbGetPreparedQuery() is deprecated, please switch to DBI::dbGetQuery(params = bind.data).Named parameters not used in query: internal_chrom_id, chrom, length, is_circularNamed parameters not used in query: internal_id, name, type, chrom, strand, start, endNamed parameters not used in query: internal_id, name, chrom, strand, start, endNamed parameters not used in query: internal_id, name, chrom, strand, start, endNamed parameters not used in query: internal_tx_id, exon_rank, internal_exon_id, internal_cds_idNamed parameters not used in query: gene_id, internal_tx_idOK

rr covData <- riboSeqFromBAM(riboFiles, txdb = TxDb)

paramScanBAM parameter is not a ScanBamParam object. Set to default NULL value!
/media/rna/public_Ribo/GSE62134/single_end/mapped/bams/SRR1605293.bam


Read alignment file


Plot match length distribution.