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Old 11-24-2016, 09:10 PM   #1
Location: Toronto

Join Date: Nov 2016
Posts: 19
Default Adaptor Removal with Trimmomatic

Hi there,

I ran a HiSeq2500 run and found that I had adaptor sequences still present.
I first used Trimmomatic to simulatenously remove the adaptor sequences and trim the sequences to a good quality score.

I want to merge the reads next but because I used the Pair-ended format for trimmomatic, I end up with 4 output files: forward paired, forward unpaired, reverse paired, reverse unpaired. How do I go about merging these files? Should I discard the unpaired files and focus on the paired? Or merge the paired together and then concatenate the unpaired? Thank you!
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