A question about cutadapt
Hi,
I am using cutadapt for the first time, and I want to make sure I do it right. I have sequences that had illumina adaptors with a barcode, so they look like this:
ADAPTORa=BARCODE=ADAPTORb
they were sequenced non-directionally, using the R-primer in reverse transcription.
what is the best way to clean it all out? I thought that I should look for ADAPTORb in both the original and the reverse complement options but now I am second guessing myself...
your help will be greatly appreaciated.
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