[khmer] slice-reads-by-coverage.py on PE data question

[C. Titus Brown]

Diane, Chris --

Hmm, the following could work if you don't mind losing orphaned reads:

interleave-reads.py => interleaved reads.

slice-reads-by-coverage.py => "broken paired" reads, where pairs remain
    next to each other but there are lots of orphans.

extract-paired-reads.py => separate into still-paired (.pe) and orphaned (.se)
    reads.

If you want to always retain the pair if either has the right coverage, that
would require modifications to the script or a more complex workflow.  While
modifying the script is probably a good idea, we may not have time to do so in
the next week or three, though.

Diane, how about this - see if you can get the workflow above to work and
give decent results (I would suggest plotting the coverage distribution of
the .pe file as one way to evaluate), and if not, we can do the script
modification for you.

--titus

On Fri, Jun 05, 2015 at 02:14:11PM +0000, Fields, Christopher J wrote:
> I have used split-paired-reads.py for this purpose when normalizing PE reads, I assume it should work the same here.
> 
> chris
> 
> On Jun 5, 2015, at 8:38 AM, Diane Hatziioanou <dianehioanou at gmail.com<mailto:dianehioanou at gmail.com>> wrote:
> 
> Hello all again,
> 
> I have a question.
> I want to use the slice-reads-by-coverage.py but I've got PE data which I would like to keep as PE data. Is slice-reads-by-coverage.py able to deal with interleaved PE data and keep it PE, can it manage it in another format or am I asking for too much and would have to use single ends and try pairing them back after its done?
> 
> Thanks,
> Diane
> 
> --
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-- 
C. Titus Brown, ctbrown at ucdavis.edu