Hello,
I'm following the RNA-seq workflow for differential gene expression
white paper by Michael Love Simon Anders and Wolfgang Huber.http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&ved=0CFcQFjAJ&url=http%3A%2F%2Fwww.bioconductor.org%2Fhelp%2Fcourse-materials%2F2014%2FBioC2014%2FRNA-Seq-Analysis-Lab.pdf&ei=_ihmVK3nMoSrNsb9gsAH&usg=AFQjCNH5FkLy2MQwoJCUSMdfb3KrrP45Yw&sig2=iUkasIDbf7SyjBSOl0BKHQ&bvm=bv.79142246,d.eXY&cad=rja

## 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!!

all the steps I did before try to create the object "se" are below

### 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);