PolyG trimming?

[mht85]

Hello,

Thanks for the program. I'm working with NovaSeq data currently and would like to try out the polyG trimming. After trimming, it looks like fastp still retains reads with 8 or less Gs at the ends of reads. Is that a default set by fastp and what is the reason for doing so? Any way I can change the number of G's fastp lets through its filter?

Cheers,
Mun

[sfchen]

Currently fastp doesn't trim polyG with G number less than 10. If you prefer a parameter to adjust this setting, I will implement it in the coming version.

[mht85]

It would be nice to have the option to adjust that setting. Would also be great to have the count included in the report? Just a suggestion. Thanks for the software by the way. May I know when the next version will be released?

[sfchen]

Next revision will come in two weeks.

[sfchen]

With the latest version in the master branch, you can use --poly_g_min_len to change the minimum length requirement for polyG detection. By default it's 10.

[sfchen]

Any update? Have you tried the new fastp, which can be compiled from the latest code, or downloaded from http://opengene.org/fastp/fastp ?