last read is skipped in htseq-count

Simon Anders — Thu, 18 Oct 2012 14:44:44 -0000

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

Recent changes to 6: last read is skipped in htseq-count