Closed manjumoorthy95 closed 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
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.
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
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.