Bismark to MethylKit
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6 months ago
Arindam Ghosh ▴ 400

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?

methylkit bismark bsseq • 328 views
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