To All DEXSeq Users, 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). Please also mention the versions of python and htseq used. The many warning messages I usually encounter basically say that the program can not find the other member of the pair. Thank you. Margaret [[alternative HTML version deleted]]

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. Simon