II need your advice
I am analyzing by WBGS (whole genome bisulfite sequencing) the genome of my plant under two conditions with 3 biological replicates each. I did run a Illumina sequencing of paired reads, and mapped the reads with both, bismark and bwameth looking for methylation in the three plant contexts, that is CpG, CHH and CHG
I am sort of confused because the methylation bias I got using any of these two mappers. Pictures shown below show that R1 reads have a nice mbias easy to supersede, whereas R2 show a increased or decreased bias along all the reads in all my samples
So I have several questions
Why this "crazy" mbias is systematically present in all my R2 reads
Is it a nice idea or not to do paired mapping when analyzing methylation?
Any idea on how to treat these three biological replicates ?. Should I average the data ?