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

Fields, Christopher J cjfields at illinois.edu
Fri Jun 5 08:30:37 PDT 2015


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



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