[khmer] orientation of SE reads

bioques bioques at 163.com
Tue Oct 1 18:12:01 PDT 2013

Hi Professor Brown,

I tried to follow the protocol you kindly offer here (https://github.com/ged-lab/khmer-protocols/tree/master/mrnaseq). It really a great help to newbie like me for RNA-Seq analysis. But I got one question about the step after trimming the adapter with Trimmomatic (document in 1-quality.txt). You suggest to combine the SE reads s1_se and s2_se together. Would this hurt the orientation of the reads when doing the assembly (I am going to use Trinity to do the assembly)? I wonder if I should convert the s2_se reads to its reverse complement before combine the two files together?

Hope to hear from you and thanks in advance!

sincerely yours,

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