[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
>> Greek Mobile: (+30)6909403373
>> UK Mobile: (+44)7779516625
>> www.linkedin.com/in/dhatziioanou/<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.linkedin.com_in_dhatziioanou_&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=dRcvnkEofGJzLdh7UkycULWyPkXIh41x5bZwerAUmho&s=HkGDnjft354ZjCH76btBvDSlqJalDCBYdlxfZezC5A4&e=>
>> https://twitter.com/DianeHIoanou<https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_DianeHIoanou&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=dRcvnkEofGJzLdh7UkycULWyPkXIh41x5bZwerAUmho&s=IXFKb657NAEdn_sXAHqCdOLY8MG2FfADm3AWWqWIMAk&e=>
>>
>> _______________________________________________
>> khmer mailing list
>> khmer at lists.idyll.org<mailto:khmer at lists.idyll.org>
>> http://lists.idyll.org/listinfo/khmer
>>
>
>> _______________________________________________
>> khmer mailing list
>> khmer at lists.idyll.org
>> http://lists.idyll.org/listinfo/khmer
>
>
> --
> C. Titus Brown, ctbrown at ucdavis.edu
More information about the khmer
mailing list