bedgraph for CHH and CHG methylation only
I am trying to generate separate bedgraph files for CHH and CHG methylation contexts like in the previous post. Th only options available in bismark seem to be CpG or All contexts when it comes to the generating the bedgraph report. I was thinking the only way to split these reports is to:
1. use the --CX option and the --cytosine_report option
2. pull out just the CHH or CHG methylation calls from the cytosine report and intersect that with the bedgraph output
I am not really sure what to do. This is older data and I already have the CHH and CHG methylation extractor files from an older version of bismark so I would rather not have to re-generate those files. Any advice is appreciated.
Thanks
I am trying to generate separate bedgraph files for CHH and CHG methylation contexts like in the previous post. Th only options available in bismark seem to be CpG or All contexts when it comes to the generating the bedgraph report. I was thinking the only way to split these reports is to:
1. use the --CX option and the --cytosine_report option
2. pull out just the CHH or CHG methylation calls from the cytosine report and intersect that with the bedgraph output
I am not really sure what to do. This is older data and I already have the CHH and CHG methylation extractor files from an older version of bismark so I would rather not have to re-generate those files. Any advice is appreciated.
Thanks
Originally posted by fkrueger
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