Bismark icon indicating copy to clipboard operation
Bismark copied to clipboard

Add cytosine context methylation totals to docs

Open FelixKrueger opened this issue 2 years ago • 1 comments

We currently don't seem to have a description of the context specific methylation totals in the new (and awesome) docs. More information on the report are here.

FelixKrueger avatar Nov 10 '22 09:11 FelixKrueger

Just as a reminder, the report looks at 2 bases downstream, as well as 1 base upstream of the C taking part in the methylation call. This is useful for looking at methylation in specific contexts (e.g. CpA only), and also when using GpC methylases that introduce methylation in GpC context

upstream	C-context	full context	count methylated	count unmethylated	percent methylation
A	CAA	ACAA	308398	93360	23.24
C	CAA	CCAA	329555	75518	18.64
G	CAA	GCAA	242262	118175	32.79
T	CAA	TCAA	302209	86219	22.20
A	CAC	ACAC	266786	91121	25.46
C	CAC	CCAC	409749	89154	17.87
...

FelixKrueger avatar Nov 10 '22 09:11 FelixKrueger