Input files for methylKit

[Rosa Icela Luna Ramirez]

Hello,

I am currently working on analyzing DNA methylation. I used Bismark protocol to identify the methylation calls. I have ten outputs, bedGraph, Bismark.cov, M-bias.txt, splitting_report.txt, two CHG.txt, two CHH.txt, and two CpG.txt. I am not sure what do I need to start the analysis on MethylKit, which data txt or bam file.

Thank you,

Rosa Luna

[Alexander Blume]

Hi Rosa, 

Please check the `pipeline` argument of the `methRead` function. 

The corresponding section describes which files you may use to load your data. 

Best, 

Alex

[pradeep battula]

Hi!

I am also struggling with the same problem. Can we use bismark.cov file for input by mentioning the argument pipeline = "bismark" ?

Thank you! 

[Alexander Blume]

Hi

Please check the details section of the function help: https://rdrr.io/bioc/methylKit/man/methRead-methods.html

Best,
Alex