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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
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bed file #23

Closed Fabunanr closed 8 years ago

Fabunanr commented 8 years ago

What does "pct" mean?

how can I tell which site is methylated?

superbobry commented 8 years ago

What does "pct" mean?

I think pct stands for percentage of C to C + T and is otherwise known as "methylation level".

how can I tell which site is methylated?

You need statistics to do that reliably, e.g. you can simply threshold "pct".

brentp commented 8 years ago

I would also mention to use https://github.com/dpryan79/PileOMeth for extraction after mapping with bwa-meth, rather than relying on the scripts here. Those are more actively developed.