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al2na / methylKit

R package for DNA methylation analysis
https://bioconductor.org/packages/release/bioc/html/methylKit.html
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Import CpG_context file to Methylkit #286

Closed manjumoorthy95 closed 1 year ago

manjumoorthy95 commented 1 year ago

Hi. I am using Bismark pipeline to process my Whole genome BS data. So after running Bismark methylation extract command I got 3 different text files for each context CpG, Chh and Chg. I know we can import the .cov or bam files to Methylkit. But what I specifically want to understand is that, is there any method where I can import the CpG_Context.txt into the Methylkit?

Kindly guide.

alexg9010 commented 1 year ago

HI @manjumoorthy95,

When you say CpG_Context.txt are you referring to the file generated with bismark_methylation_extractor --cytosine_report? If yes, this can be read by using methRead with the pipeline argument set to "bismarkCytosineReport".

If this is not how the file was generated, it would be great if you could specify how this file was created.

Best, Alex

manjumoorthy95 commented 1 year ago

No..these context specific files gets generated from the Bismark extract command when we use --comprehensive argument. A file gets generated for each context CpG , CHh and Chg.

alexg9010 commented 1 year ago

I see. No, the default output format generated by the bismark_methylation_extractor is not supported by methylKit. These files summarize methylation calls on the read level, but we require per-locus information.

Best, Alex