<div dir="ltr">I've never had a problem before, but then again I've either (a) explicitly made sure R1 & R2 were in that order or (b) sorted the files (which usually puts them in the right order)<div><br></div><div>In a script I wrote over the holidays, I forgot to do this & half the runs it worked & half it failed. And then I substituted '/path/to/fastq/*.fastq.gz' and they all worked -- which had me scratching my head until this morning when it hit me I hadn't sorted them before!</div><div><br></div><div>So, my trying to make you do some work & take a performance hit to prevent something simply sorting the list of input files would accomplish! :-)<br><div><br></div><div>More seriously, perhaps interleave-reads.py could do the swap automatically</div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Dec 30, 2015 at 10:01 AM, C. Titus Brown <span dir="ltr"><<a href="mailto:ctbrown@ucdavis.edu" target="_blank">ctbrown@ucdavis.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="HOEnZb"><div class="h5">On Wed, Dec 30, 2015 at 10:00:49AM -0500, Keith Robison wrote:<br>
> Probably few people would see this as a bug, but is_pair in utils.py (and<br>
> by extension, interleave_pairs.py) is sensitive to the order the two<br>
> sequences are given in -- if you give sequences (FASTQ files for<br>
> interleave_pairs.py) in the order R2, R1, the function will say they are<br>
> not paired<br>
<br>
</div></div>It certainly is! Are there programs that accept R2 before R1?<br>
<br>
best,<br>
--titus<br>
</blockquote></div><br></div>