I have used Bismark for aligning RRBS reads and now I should run methylKit on bismarks' output, like CpG and bedGraph and .Cov. How can I use these files instead of bam file.
Methylkit manual said it accepts bismark bam file however, I could not handle it. It gives error when I used bismark sorted bam files, and methRead function does not work too.
Does anybody know pipeline for working with bismark output files? I don't mean bam/sam.