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Removal of degenerated primers in --adaper_fasta file #470

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BIOMOL-ANFACO opened this issue Mar 16, 2023 · 1 comment
Open

Removal of degenerated primers in --adaper_fasta file #470

BIOMOL-ANFACO opened this issue Mar 16, 2023 · 1 comment

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@BIOMOL-ANFACO
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BIOMOL-ANFACO commented Mar 16, 2023 •
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Hi,

I have been reviewing the fastp documentation and I can't find if this software supports degenerate primers removal, that is, if fastp recognizes the IPAC degenerate codes in the primers file that we are using through "--adapter_fasta" option included in fastp. The problem is that the PCR primers that we have in the "--adapter_fasta" file are not being removed from the PE reads. The primers include several degenerate positions.

Has anyone had this problem?
Thanks in advance for any responses/comments.

Regards
@nvpatin
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nvpatin commented Dec 4, 2023

I got an error when I tried to input primers with degenerate bases into fastp. From what I can tell the program only supports A,T,C, and G for the adapter (primer) sequences.

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@nvpatin @BIOMOL-ANFACO