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Old 11-13-2014, 06:45 PM   #1
colaneri
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Location: Durham

Join Date: Jul 2012
Posts: 30
Default summarizeOverlaps error

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
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!!
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