last read is skipped in htseq-count
Analysing high-throughput sequencing data with Python
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Thomas A. wrote on 2012-10-15:
Hi Simon,
I've run into an a minor issue with htseq-count.
Essentially, the last read-pair is missing from the counts.
This issue was described before and should be fixed, in 0.5.3p1, however, I'm running 0.5.3p9 and I am missing the final fragment.
http://seqanswers.com/forums/showthread.php?t=15329
Any idea what's going on?
My command line:
htseq-count -s reverse -m intersection-nonempty -t transcript_unit -o <output> -i <input> <gtffile>
cheers,
Thomas