Which is the correct file to be taken from Bismark to methylKit?
The primary option would be to read in the SAM/BAM files and perform methylation calling in methylKit. However, it can also be done through
bismark_methylation_extractor which produces context (CpG/CHG/CHH) dependent methylation call files containing the following columns:
<seq-ID> <methylation state*> <chromosome> <start position (= end position)> <methylation call>
This is not the expected input methylation call file as required by methylKit. As per the tutorial, a typical methylation call file should look like:
chrBase chr base strand coverage freqC freqT
Other options include creating bedGraph coverage file or cytosine report.
So which of the possible output files from Bismark be taken into methylKit?