[khmer] Fwd: About Khmer and Trinity.
Won C Yim
wyim at unr.edu
Thu Jan 16 11:01:49 PST 2014
Dear Brown,
Hi!
I have question.
I have a 114 reads data.
First I ran Trinity with whole dataset with adapter and quality trimmed fastq.
The no. of contigs were 108,112 .
After your normalization it generated 22,454 contigs.
I know it works well but our species has 295Mb.
The Ararbidopsis is 135Mb and have 30,000 genes.
I think 22,454 contigs were to small.
Do I lost something?
Please help.
Thank you.
> 보낸 사람: "Yim,Won Cheol" <wyim at unr.edu>
> 제목: Re: About Khmer and Trinity.
> 날짜: January 15, 2014 at 2:02:35 PM PST
> 받는 사람: "<titus at idyll.org>" <titus at idyll.org>
>
> Dear Brown,
>
> Hi!
>
> I have question.
>
> I have a 114 reads data.
>
> First I ran Trinity with whole dataset with adapter and quality trimmed fastq.
>
> The no. of contigs were 108,112 .
>
> After your normalization it generated 22,454 contigs.
>
> I know it works well but our species has 295Mb.
>
> The Ararbidopsis is 135Mb and have 30,000 genes.
>
> I think 22,454 contigs were to small.
>
> Do I lost something?
>
> Please help.
>
> Thank you.
>
> Won
> __
> Yim, Won Cheol
>
> Postdoctoral Fellow
>
> MS330/Department of Biochemistry & Molecular Biology
> 1664 N. Virginia Street
> University of Nevada
> Reno, NV 89557-0330
>
> Mobile:775-229-0453
> Email: wcyim at unr.edu
> http://ascendo.u.googlepages.com
>
> Jan 10, 2014, 5:29 AM, C. Titus Brown <ctb at msu.edu> 작성:
>
>> Hi Won, the k-mer size is not directly analogous. We've had fine experience
>> with k=20.
>>
>> best,
>> --titus
>>
>> On Fri, Jan 10, 2014 at 06:19:21AM +0000, Won C Yim wrote:
>>> Dear Titus,
>>>
>>> Hi!
>>>
>>> I have a question for your tutorial.
>>>
>>> I think Trinity use 25mer for assembly.
>>>
>>> Is it Okay to use 20mer for kmer?
>>>
>>> Thank you.
>>>
>>> Won
>>> __
>>> Yim, Won Cheol
>>>
>>> Postdoctoral Fellow
>>>
>>> MS330/Department of Biochemistry & Molecular Biology
>>> 1664 N. Virginia Street
>>> University of Nevada
>>> Reno, NV 89557-0330
>>>
>>> Mobile:775-229-0453
>>> Email: wcyim at unr.edu<mailto:wcyim at unr.edu>
>>> http://ascendo.u.googlepages.com
>>>
>>> 2013. 12. 18., ???? 10:45, C. Titus Brown <ctb at msu.edu<mailto:ctb at msu.edu>> ????:
>>>
>>> Hi Won,
>>>
>>> https://khmer-protocols.readthedocs.org/en/v0.8.4
>>>
>>> best,
>>> --titus
>>>
>>> On Wed, Dec 18, 2013 at 06:38:18PM +0000, Won C Yim wrote:
>>> Dear Titus Brown,
>>>
>>> Hi !
>>>
>>> I am Won Cheol Yim in University of Nevada, Reno.
>>>
>>> Recently, I try to de novo assemble one of plant species (~350Mb) by using RNA-seq data.
>>>
>>> I already assembled by Trinity alone and Trinity normalization program.
>>>
>>> But the result is too bad.
>>>
>>> Actually we have deep sequencing (250GB of 100bp Illumina single read).
>>>
>>> So there is so many weird contigs.
>>>
>>> I read many things about that like cut-off based on FPKM and Isoform percent.
>>>
>>> However there??s no answer.
>>>
>>> I think Khmer can help my dataset.
>>>
>>> Is it possible to use Khmer with Trinity.
>>>
>>> There is no reference paper.
>>>
>>> And Trinity use 25 kmer as default.
>>>
>>> Can you advice me the critical options?
>>>
>>> I??ve used ?? normalize-by-median.py -k 20 -C 20 --hashsize 2e9 --n_hashes 4 all.fastq ??
>>>
>>> My fastq file is already trimmed by Q>20 and illumina adaptors.
>>>
>>> Would you mind advice me some helpful comment?
>>>
>>> Thank you.
>>>
>>> Won
>>>
>>>
>>>
>>> __
>>> Yim, Won Cheol
>>>
>>> Postdoctoral Fellow
>>>
>>> MS330/Department of Biochemistry & Molecular Biology
>>> 1664 N. Virginia Street
>>> University of Nevada
>>> Reno, NV 89557-0330
>>>
>>> Mobile:775-229-0453
>>> Email: wcyim at unr.edu
>>> http://ascendo.u.googlepages.com
>>>
>>>
>>> --
>>> C. Titus Brown, ctb at msu.edu
>>>
>>
>> --
>> C. Titus Brown, ctb at msu.edu
>
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