Question: Paired-end imports produce 8 files. What to do?
gravatar for chrissie
10 months ago by
chrissie10 wrote:

Hi all, I've been scouring the forum for the "first step" in importing fastaq.gz (which unzips automatically) because when I import I get 8 separate files (R1 and R2 for each of the 4 lanes). I intend to run Trinity to construct a de novo assembly, and require that the paired-ends remain separate. So far, I perform QC --> FastGroomer (to convert) --> Trimmomatic --> QC again. But these steps are performed on my 8 files individually.

Q1. Should I merge (Text Manipulation, tail-to-end) all R1 and all R2s of the same sample together, then perform QC-trim-QC?

I have 10 paired-end samples altogether, and need to run the de novo assembly using all of these. I read somewhere that ALL R1 (i.e. from all 10 samples) should be merged, and ALL R2 should be merged to make 2 files. I thought I uploads each sample separately, and I can't find where I read that.

Q2: Should I merge ALL 10 samples R1 together for Trinity?

I'm a total technophobe and I'm so concerned I'll do something wrong for my PhD.

Thank you Biostar community for your help!

assembly galaxy rna-seq • 247 views
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