Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
summarizeOverlaps error Parharn Bioinformatics 11 06-09-2014 10:12 AM
Tophat Error: Error: segment-based junction search failed with err =-6 sjnewhouse RNA Sequencing 8 03-19-2013 05:14 AM
Tophat 2 error: Parse error at line 297359: missing colon in auxiliary data magbju RNA Sequencing 2 01-15-2013 04:57 AM
tophat2 segment_juncs error: Error: segment-based junction search failed with err =-6 Bioinformatics 1 04-16-2012 07:37 AM
summarizeOverlaps vs countOverlaps swaraj Bioinformatics 0 02-29-2012 09:42 AM

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

Join Date: Jul 2012
Posts: 30
Default summarizeOverlaps error

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
### 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


##### Use the BamFile function from the RsamTools to se if these paths are functional

library ("Rsamtools");

#Counting reads in genes


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
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!!
colaneri is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 04:41 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO