[protocols] 答复: 答复: Khmer troubleshooting

[Michael R. Crusoe]

On Mar 24, 2014 10:38 AM, "Shu CHEN" <szc0049 at tigermail.auburn.edu> wrote:

>
> Hi, Michael,
>

Hello Shu. While I have used the khmer-protocols I'm mainly work on khmer
itself. The quickest way to get support with the khmer protocols is to
email the mailing list: protocols at lists.idyll.org (which I've CC'd)

> This is Shu from Dr. McElroy's lab. I am trying to use khmer to diginorm
my illumina data and I have some questions about it:
>
> 1. I diginormed my data following the Eel Pond mRNAseq Protocol. The N50
of the assembly is 1242, smaller than the assembly from the non-diginormed
data, and also the number of the contigs is half of the non-diginormed. Is
this normal that both assembly size and N50 becomes smaller?
>
> 2. Because I got the data with adapter trimmed off, so I passed the step
1 and directly went to the interleave step. Does this cause any problems in
the downstream process?
>
> 3. After splitting the *.pe file into left.fq and right.fq, the left.fq
has a size of 1.7gb, and thr right.fq 1.4gb. Is this okay?
>
> Thank you very much. I appreciate your time and patience.
>
>
>
>
> Shu Chen
>
> Ph.D. Student
>
> Department of Agronomy and Soils
>
> RM 165, Funchess Hall
>
> ________________________________
> 发件人: Michael R. Crusoe <mcrusoe at msu.edu>
> 发送时间: 2014年3月4日 2:36
> 收件人: Shu CHEN
> 抄送: Leigh Sheneman; khmer at lists.idyll.org
> 主题: Re: 答复: Khmer troubleshooting

-- 
Michael R. Crusoe:  Programmer & Bioinformatician   mcrusoe at msu.edu
 @ the Genomics, Evolution, and Development lab; Michigan State U
http://ged.msu.edu/ http://orcid.org/0000-0002-2961-9670
@biocrusoe<http://twitter.com/biocrusoe>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.idyll.org/pipermail/protocols/attachments/20140326/324557aa/attachment.htm>