Question: Paired-end imports produce 8 files. What to do?
1
gravatar for chrissie
17 months ago by
chrissie10
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 • 395 views
ADD COMMENTlink written 17 months ago by chrissie10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 170 users visited in the last hour