I am confused about bisulfite converted library GC content.
Fastqc per base sequence content looks like this:
(%G has decreased and %A has increased, compared to reference genome).
1. Shouldn't %C have decreased instead of %G?
Bismark reports that >90% C's in CHG and CHH were methylated, however people from the wet lab say that in this organism only CpG methylation is possible.
2. Seeing such result (methylation in CHH and CHG) can we speculate that something went bad with bisulfite conversion?
3. Bismark/BS Seeker2 maps only those reads that have non-converted Cs (this is way we get high CH methylation percentage). What can be the reason that reads with converted Cs don't map?