Recent changes to 6: last read is skipped in htseq-counthttps://sourceforge.net/p/htseq/bugs/6/2012-10-18T14:44:44ZRecent changes to 6: last read is skipped in htseq-countlast read is skipped in htseq-count2012-10-18T14:44:44Z2012-10-18T14:44:44ZSimon Andershttps://sourceforge.net/u/userid-794651/https://sourceforge.net1d7727c7317bbca1fe9a27901e942d3e3174add5<div class="markdown_content"><p>Thomas A. wrote on 2012-10-15:</p>
<p>Hi Simon,</p>
<p>I've run into an a minor issue with htseq-count.</p>
<p>Essentially, the last read-pair is missing from the counts.</p>
<p>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.<br />
<a href="http://seqanswers.com/forums/showthread.php?t=15329" rel="nofollow">http://seqanswers.com/forums/showthread.php?t=15329</a></p>
<p>Any idea what's going on?</p>
<p>My command line:<br />
htseq-count -s reverse -m intersection-nonempty -t transcript_unit -o <output> -i <input> <gtffile></p>
<p>cheers,<br />
Thomas </p></div>