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FelixKrueger / Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states
http://felixkrueger.github.io/Bismark/
GNU General Public License v3.0
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Add cytosine context methylation totals to docs #542

Closed FelixKrueger closed 1 year ago

FelixKrueger commented 1 year ago

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 commented 1 year ago

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
...