search

brentp / bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
https://arxiv.org/abs/1401.1129
MIT License
139 stars 53 forks source link

Disallow RC alignments #9

Closed superbobry closed 10 years ago

superbobry commented 10 years ago

Bowtie has --norc option

If --norc is specified, bowtie will not attempt to align against the reverse-complement reference strand.

I'm not aware of a similar option for BWA, but I think it makes sense as a default strategy for bs-seq alignments, because the reads from the reverse strand don't add any extra information in terms of methylation status.

What do you think?

superbobry commented 10 years ago

Actually, after some thought I've convinced myself this is a bad idea. Closing.