Is it possible to remove overrepresented sequence from trimgalore?

Question

[yosapol.harn]

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

[swbarnes2]

What have you tried? Indicating the sequence you want to trim in your command line? Adding your sequence to the database?

[yosapol.harn]

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

[Hyper_Odin]

But, why do you want to remove them? If you remove them, you may risk removing some of the over-expressed genes!

[GenoMax]

From original post:

These sequences were indicated as a long primer which is not in trimgalore database.

[Lila M]

Have you tried [bbduck][1]?

bbduk.sh -Xmx4g in=file.fa  out=clean_file.fa ktrim=r k=21 ref=/pathTo/adapters.fa