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BSSeeker / BSseeker2

A versatile aligning pipeline for bisulfite sequencing data
http://pellegrini.mcdb.ucla.edu/BS_Seeker2/
MIT License
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Understanding methylation C in mapped reads #33

Open Surajuvm opened 4 years ago

Surajuvm commented 4 years ago

Hello Weilong,

I just wanted to confirm that I have understood these numbers correctly. Below is a part of log file obtained after mapping; using bs_seeker2-align.py

Methylated C in mapped reads 
mCG  67.190%
mCHG 0.836%
mCHH 0.851%

My understanding is that within the mapped reads; 67.190% of cytosines present in CG context are methylated. 0.836% of cytosines present in CHG context are methylated and so on.

These numbers have nothing to do with the level of methylation, right? We get the methylation level only after calling methylation; using bs_seeker2-call_methylation.py

Please let me know if I am missing something.

Thank you, Suraj