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jsh58 / DMRfinder

Identifying differentially methylated regions from MethylC-seq (bisulfite-sequencing) data
MIT License
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Can I use customized region for finding significant DMR? #11

Closed Honchkrow closed 4 years ago

Honchkrow commented 4 years ago

Hello, I am interested in using your tool for finding significant CpG island between case and control. Can I use customized region for finding significant DMR? I mean changing combined.csv to customized region file like CpG island. If it is possible, what's the format (which column combined.csv needs to contain) should I create. Thanks for your help! Honchkrow

jsh58 commented 4 years ago

Thanks for the question. Yes, you can filter your csv file before running findDMRs.r. To select only regions overlapping a reference, I would recommend a tool such as bedtools.

The format of the input file for findDMRs.r is given under the description of the -i <input> argument here.

Honchkrow commented 4 years ago

Thanks for your reply.