[khmer] k-mer size

[C. Titus Brown]

Hi Marsel,

we've had success with the range 21-31 -- please see:

https://khmer-protocols.readthedocs.io/en/ctb/mrnaseq/index.html

which uses 21.

best,
--titus

On Sat, Oct 29, 2016 at 10:28:57PM +0700, Marsel R. Kabilov wrote:
> Dear Titus,
>
> Thank you for your reply.
> I would like to normalize data for transcriptome de novo assembly.
> But the main question is how can I understand what ksize normal for this  
> data.
>
> Best wishes,
> Marsel
>
> 29.10.2016 22:21, C. Titus Brown ??????????:
>> Hi Marsel,
>>
>> this will depend on your application. What are you trying to do?
>>
>> For most applications of khmer we use between 21 and 31.
>>
>> best,
>> --titus
>>
>> On Thu, Oct 27, 2016 at 06:22:50PM +0700, Marsel R. Kabilov wrote:
>>> Dear colleagues,
>>>
>>> I have question about size of k-mer (--ksize parameter) for
>>> normalize-by-median.py.
>>> I don't find anything about choosing of k-mer size.
>>> Would you so kind to help me?
>>>
>>> Sincerely yours,
>>> Marsel
>>>
>>> ---------------------------------------------------------------------
>>> Marsel Kabilov, Ph.D.
>>> Head of SB RAS Genomics Core Facility
>>> Institute of Chemical Biology and Fundamental Medicine SB RAS
>>> Lavrentiev av. 8, Novosibirsk, 630090, Russia
>>> Tel.: +7 383 3635113
>>> Fax: +7 383 3635153
>>> sequest.niboch.nsc.ru
>>>
>>> _______________________________________________
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>

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