Position of all cytosines in retention pattern

[shahmj]

Hi,

In the single-end epiread format one of the fields in the output is "5) position of the cytosine in the first CpG (0-based)". Is it somehow possible to get length of the alignment or position of remaining cytosines for all CpGs covered by the read? I would like to consider CpGs within a certain distance from the first one.

Thanks,
Minita