<div dir="ltr"><p dir="ltr"><br></p><p>On Mar 24, 2014 10:38 AM, "Shu CHEN" <<a href="mailto:szc0049@tigermail.auburn.edu" target="_blank">szc0049@tigermail.auburn.edu</a>> wrote:<br>
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> Hi, Michael,<br>
></p><p dir="ltr">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: <a href="mailto:protocols@lists.idyll.org" target="_blank">protocols@lists.idyll.org</a> (which I've CC'd)</p>
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> 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: <br>
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> 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?<br>
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> 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?<br>
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> 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?<br>
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> Thank you very much. I appreciate your time and patience.<br>
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> <br>
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> Shu Chen<br>
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> Ph.D. Student<br>
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> Department of Agronomy and Soils<br>
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> RM 165, Funchess Hall<br>
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> ________________________________<br>
> 发件人: Michael R. Crusoe <<a href="mailto:mcrusoe@msu.edu" target="_blank">mcrusoe@msu.edu</a>><br>
> 发送时间: 2014年3月4日 2:36<br>
> 收件人: Shu CHEN<br>
> 抄送: Leigh Sheneman; <a href="mailto:khmer@lists.idyll.org" target="_blank">khmer@lists.idyll.org</a><br>
> 主题: Re: 答复: Khmer troubleshooting<br></p><div><br></div>-- <br><div dir="ltr"><span style="font-family:'courier new',monospace;font-size:small">Michael R. Crusoe: Programmer & Bioinformatician </span><a href="mailto:mcrusoe@msu.edu" style="color:rgb(17,85,204);font-family:'courier new',monospace;font-size:small" target="_blank">mcrusoe@msu.edu</a><br style="font-family:'courier new',monospace;font-size:small">
<span style="font-family:'courier new',monospace;font-size:small"> @ the Genomics, Evolution, and Development lab; Michigan State U</span><br style="font-family:'courier new',monospace;font-size:small"><a href="http://ged.msu.edu/" style="color:rgb(17,85,204);font-family:'courier new',monospace;font-size:small" target="_blank">http://ged.msu.edu/</a><span style="font-family:'courier new',monospace;font-size:small"> </span><a href="http://orcid.org/0000-0002-2961-9670" style="color:rgb(17,85,204);font-family:'courier new',monospace;font-size:small" target="_blank">http://orcid.org/0000-0002-2961-9670</a><span style="font-family:'courier new',monospace;font-size:small"> </span><a href="http://twitter.com/biocrusoe" style="color:rgb(17,85,204);font-family:'courier new',monospace;font-size:small" target="_blank">@biocrusoe</a><br>
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