M-bias: CHH and CHG total calls drop off in Read2
Hi Everyone,
I have questions regarding M-bias plot and CHH,CHG methylation calls generated with bismark. I hope it is the right thread to ask otherwise let me know where should have I posted it.
Has anyone seen a drop off of CHH and CHG total calls within a M-bias plot generated by bismark tool?
I have observed this drop off only in the M-bias read2 plot.
(See Attached png plots)
The data are from Whole Genome BiSulphite with reads of 101 bases
Library Prep was performed using Ultralow Ovation MS kit.
How to interpret the falling number of calls after 50 bases? and ....
How this can impact the alignment of read2 in bismark? and the Methylation calls?
Thanks for your help,
Christophe
Hi Everyone,
I have questions regarding M-bias plot and CHH,CHG methylation calls generated with bismark. I hope it is the right thread to ask otherwise let me know where should have I posted it.
Has anyone seen a drop off of CHH and CHG total calls within a M-bias plot generated by bismark tool?
I have observed this drop off only in the M-bias read2 plot.
(See Attached png plots)
The data are from Whole Genome BiSulphite with reads of 101 bases
Library Prep was performed using Ultralow Ovation MS kit.
How to interpret the falling number of calls after 50 bases? and ....
How this can impact the alignment of read2 in bismark? and the Methylation calls?
Thanks for your help,
Christophe
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