Hello,
I'm following the RNA-seq workflow for differential gene expression
white paper by Michael Love Simon Anders and Wolfgang Huber.
This is the code
however I got this error and I have not idea how to fix it:
Error in .summarizeOverlaps_BamFileList(features, reads, mode, ignore.strand = ignore.strand, :
duplicate 'names(reads)' not allowed
Can someone help please!!
I'm following the RNA-seq workflow for differential gene expression
white paper by Michael Love Simon Anders and Wolfgang Huber.
This is the code
Code:
### read the table: sampleTable.csv sampleTable <- read.csv("sampleTable.csv", header=TRUE); ### build the full path to the tophat produced bam files bamFiles <- file.path(".", sampleTable$dirName, sampleTable$fileName); ### see the created vector with paths bamFiles ##### Use the BamFile function from the RsamTools to se if these paths are functional library ("Rsamtools"); seqinfo(BamFile(bamFiles[1])); #Counting reads in genes library("GenomicFeatures"); hse <-makeTranscriptDbFromGFF("/proj/seq/data/TAIR10_Ensembl/Annotation/Genes/genes.gtf", format="gtf") exonsByGene <- exonsBy(hse, by="gene"); ## Use the function summarizeOverlaps to count reads in the gene library("GenomicAlignments") se <- summarizeOverlaps(exonsByGene, BamFileList(bamFiles), mode="Union", singleEnd=TRUE, ignore.strand=FALSE, fragments=FALSE);
however I got this error and I have not idea how to fix it:
Error in .summarizeOverlaps_BamFileList(features, reads, mode, ignore.strand = ignore.strand, :
duplicate 'names(reads)' not allowed
Can someone help please!!