Hello BioStar friends!
I've gotten so much help here previously and I'm looking forward to help here again!
I'm trying to use DEXSeq (a Bioconductor package) to identify and quantitate changes in splicing following expression of a transgene. I've performed the mapping of my Illumina paired-end data using BWA and now have SAM files. No problems up to this point.
The problem occurs when I run dexseq_count.py, a Python script associated with the DEXSeq package which is dependent on HTSeq in Python. I keep getting the following messages:
"UserWarning: Read HWUSI-EAS381R:1:10:12325:4848#CGATGT claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?)"
After a couple of searches I've found that HTSeq seems not to like BWA-generated SAM files. What I have not found was a work-around for this (although some people write things like "I wrote a perl script to get around this problem" with no further details).
I can use Bowtie (which is recommended), but we have a BWA Convey system so the speed up would be phenomenal, and I have quite a few of these.
Can someone help me with this?
Thanks in advance,