Is it worth mapping bisulfite reads (WGBS) to a reduced size genome?
I'm interested only in modifications in CpG context, thus instead of mapping to a whole genome (human genome) I would:
- Extract DNA sequence around each CpG (-1000/+1000 bp)
- Map reads (using bismark) to this subset
My idea is to reduce mapping time, however afraid that there might be some mapping bias or other issues.