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

[C. Titus Brown]

My suggestion: try diginorm and/or error correction.

--titus

On Fri, Jun 05, 2015 at 03:30:37PM +0000, Fields, Christopher J wrote:
> Cool, that does seem like a better path!  Thanks Titus.
> 
> We have been planning on trying something like this on a particularly thorny plant genome assembly that's been on our back-burner for a bit.  We???ve been nicknaming it ???Nessie???, primarily b/c the kmer distribution resembles fuzzy pics of the Loch Ness monster (has at least three significant peaks).  Probably a nasty combination of being highly heterozygous and having large-scale genome duplications; it???s supposed to be diploid but then again we know how that sometimes turns out w/ plants.  
> 
> chris
> 
> > On Jun 5, 2015, at 9:44 AM, C. Titus Brown <ctbrown at ucdavis.edu> wrote:
> > 
> > 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
> >> 
> >> --
> >> Dr Diane Hatziioanou
> >> Greek Mobile: (+30)6909403373
> >> UK Mobile: (+44)7779516625
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> >> 
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> > 
> > -- 
> > C. Titus Brown, ctbrown at ucdavis.edu
> 

-- 
C. Titus Brown, ctbrown at ucdavis.edu