Is it possible to remove overrepresented sequence from trimgalore?
Dear all,
After trimming the adaptor, my RNA-seq samples still contain a lot of overrepresented sequences. These sequences were indicated as a long primer which is not in trimgalore database.
Would it be possible to remove this overrepresented sequence using the function in trimgalore? I can only find -a for trimming adaptor, but not removing overrepresented sequences.
Thank you very much.
Best regards, Yosapol
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Lila M
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yosapol.harn •
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yosapol.harn •
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What have you tried? Indicating the sequence you want to trim in your command line? Adding your sequence to the database?
Hi swbarnes,
Thank you very much for replying. I have added the sequence that I would like to trim in the command line. It seems to be the sequence was only partially cut.
Would it be possible to add a list of overrepresented sequences and remove it by trimgalore?
Thank you very much
But, why do you want to remove them? If you remove them, you may risk removing some of the over-expressed genes!
From original post:
Have you tried
[bbduck][1]?