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Old 08-05-2016, 12:55 AM   #130
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Location: Cambridge, UK

Join Date: Sep 2009
Posts: 614

As long as you merged the R1 and R2 files in the same order (e.g. R1_rep1 R1_rep2, R2_rep1 R2_rep2) it shouldn't matter if you run Trim Galore on the merged files directly or run it first and merge then. All the best!
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