5' Adapter Trimming

[donutbrew]

Can I request 5' adapter/primer trimming (forgive me if I missed it in the docs):

e.g. If a primer sequence is AACTGCC:

Before: 5'-aatgaAACTGCCactgggagagagccatcattgatcgtagctg-3'
After:              5'-actgggagagagccatcattgatcgtagctg-3

This, in combination with the regular 3' trimming would be awesome.

[sfchen]

Did you mean to remove some pattern sequence inside the reads?

[donutbrew]

Scan from 5' end to find a given sequence, then trim that sequence AND everything to the left. This is useful for times when you are sequencing amplicons and you want to be sure and trim the primer sequences. I edited the example above for hopefully more clarity.

[donutbrew]

@sfchen - Did my clarification make sense? (I know it's been a while, but I wanted to see what you think about this feature.)

[obenno]

Hi @sfchen,

Thank you for the awesome program, it's pretty fast with modern visualizations.

I've the same request here, it will be great to have a feature to trim the 5' adapter sequence (TSO) just like cutadapt's -g/-G option.

obenno