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Old 06-28-2017, 12:21 PM   #1
Tommi
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Location: Switzerland

Join Date: May 2014
Posts: 1
Default Sequence Bias in Bisulphite Sequencing Mapped Reads

Hello,

I have created a post also in Biostars but the community did not have an answer to my post so I will try here. (here is the question in biostars https://www.biostars.org/p/259801/)

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 CpG Methylation at the 3'end as well as the CHH total and CHG in the total call. 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....User_Guide.pdf )

Any comment is really appreciated.
Cheers
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