mismatches allowed in adapter trimming

[hrehrauer]

Dear all Thanks for making this great tool available.

Maybe, I missed it in the documentation but I can't seem to find a description of how many mismatches you allow when trimming adapters. So my question is: If I explicitely specify a set of adapter sequences, what is the similarity criterion that must be fulfilled in order to trim the adapters?

Best regards Hubert

[sfchen]

Currently, one mismatch is allowed for every 8 bases.

I may expose a parameter to optionally set it.

[hrehrauer]

thanks. That would be helpful.

hubert

[MayLiu27]

Hello,

I notice there's the PR for this issue and probably it's already implemented, could you point me to how to set the allowed mismatch parameter for adaptor trimming for Single-end sequencing?

Many Thanks May