[protocols] Questions about mRNAseq data diginorm

[Shu CHEN]

Hi,


 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
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