Chromosomes effected by methylation about methyldackel HOT 4 CLOSED

1. That appears to be the methylation bias output, which is the text version of plots like https://camo.githubusercontent.com/95b03c9e48fbc805138562571b7a326c5636ddce29b2cc62ee57e4b366040982/68747470733a2f2f7261776769742e636f6d2f64707279616e37392f4d657468796c4461636b656c2f6d61737465722f6578616d706c655f4f542e737667 I assume nf-core put the actual methylation metrics elsewhere.
2. That is all of the chromosomes, which you need to look at to know if there are portions of your reads that should be ignored.

from methyldackel.

Ask the nf-core folks where to find the actual per-base methylation metrics. They're normally named something_CpG.bedGraph, but they may have changed that.

from methyldackel.

Well. I know the file you refer. In my test it's named 5_BKDL220006759-1a.sorted.markDups_CpG.bedGraph and looks like the following:

track type="bedGraph" description="5_BKDL220006759-1a.sorted.markDups CpG methylation levels"
chr1 16555 16556 100 1 0
chr1 16570 16571 100 1 0
chr1 16617 16618 100 1 0
chr1 16619 16620 100 1 0
chr1 16634 16635 100 1 0
chr1 16646 16647 100 1 0
chr1 16665 16666 100 1 0
chr1 16667 16668 100 1 0
chr1 17378 17379 100 1 0

So, if I well understand, this is the file containing the methylation metrics needed for further analysis.
Thank you

from methyldackel.

Correct, glad things got cleared up!

from methyldackel.