[BioC] DEXSeq: Paired End Analysis

Simon Anders anders at embl.de
Sat Oct 5 23:15:10 CEST 2013

Hi Margaret

On 05/10/13 18:01, Margaret Linan wrote:
> I have BAM files which were created using Tophat.
> While I was able to create then sort my SAM files. I have been unsuccessful
> in getting the standard paired end code to work using python and htseq.
> Can anyone share the code they use to sort their SAM file and to
> successfully run the paired end analysis (to generate COUNTS files).

Usually, TopHat SAM files work without problem. Are you sure you sorted 
the SAM file by read name (not by position)? I usually use "samtools 
sort -n" for this.

What dexseq-count.py expects is that each read is followed by its mate 
in the subsequent line of the SAM file. You could take one of the 
warning message and double-check by inspecting the SAM file whether this 
is really not the case.


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