I have performed with Bismark the M-Bias Plot and my reads looks as follow.
as far as I am understanding the end of read 1 is showing a decrease in the Methylation at the 3'end for CHG and CHH total call (orange and green colors respectively). The strange thing is the read 2 in which I can observe a drop Immediately after the first 5 nucleotides for all the type of of Methylation combination (CHH total, CHG total, CHH methylation etc..). How should I have to interpret this? To me it sounds like the read 2 look quite bad in therms of nucleotide composition, and only the CpG methylation bias is showing a good pattern. Does anyone has experienced a similar problem?
In the bismark tutorial they clearly show that Read1 and Read2 have similar pattern (see here at page 16 https://www.bioinformatics.babraham.ac.uk/projects/bismark/Bismark_User_Guide.pdf )
Any comment is really appreciated. Cheers