Hello,

I'm following the RNA-seq workflow for differential gene expression white paper by Michael Love, Simon Anders, and Wolfgang Huber (https://www.bioconductor.org/help/course-materials/2014/BioC2014/RNA-Seq-Analysis-Lab.pdf)

This is what I'm doing:

## 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!!

Here are all the previous step before trying to create the object se

### 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);