Is read trimming needed for WGBS (bisulfite) data?
1
0
Entering edit mode
5.1 years ago

These days read trimming is generally unnecessary in both DNA and RNAseq. Is there any reason why the same shouldn't be true of bisulfite-treated WGBS data?

FWIW, we're typically using biscuit for alignments (https://github.com/zwdzwd/biscuit), which is based on bwa-mem.

wgbs bisufite trimming alignment • 1.9k views
ADD COMMENT
2
Entering edit mode
5.0 years ago

Yes, we typically trim reads for WGBS even when using local alignment (bwa-meth in our case). The primary reason is that coverage for WGBS tends to be low-ish and we don't want to chance parts of the adapter getting aligned and used for methylation extraction. With fastp and recent cutadapt changes (it's finally multithreaded) at least the trimming step doesn't take seemingly forever anymore.

ADD COMMENT

Login before adding your answer.

Traffic: 1861 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6