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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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MethylKit and Methylation Data from PacBio sequence #308

Closed olaraym closed 9 months ago

olaraym commented 9 months ago

Hi @al2na, I wanted to inquire if MethylKit package can be used to run Differential methylation analysis for methylation call data obtained from hifi reads.

DavYang commented 9 months ago

Hi @al2na , I recently came across your section on segmentation and differential methylation analysis and was curious about the same thing.

alexg9010 commented 9 months ago

Hi @olaraym and @DavYang,

I did not work with hifi-reads / pacBio data myself, but the methRead function supports reading generic file types via the pipeline argument. You may check the details and examples of the methRead help.

So, if you can get per-base methylation call data (probably using pb-CpG-tools?) you should be able to import this into methylKit.

@DavYang One thing that you have to consider is that methylKit was not designed with long reads in mind, so especially for segmentation or haplotype-aware analysis you may be better off using a tool supporting read-level-based analysis, such as pycometh for ONT or ccsmethphase for PacBio.

I hope this helps, but if you have more general questions please also consider posting them on the discussion forum.

Best, Alex