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nanoporetech / modkit

A bioinformatics tool for working with modified bases
https://nanoporetech.com/
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Can you please suggest me ..How can I visualized differential methylation result? #199

Open saky7009 opened 5 months ago

ArtRand commented 5 months ago

Hello @saky7009,

Are you using the --segment option, --regions or simply single-site analysis? In general modkit doesn't have any visualization tools in it (yet). What we do, in general, is to look for places of densely clustered differentially modified bases on a viewer such as IGV. If you're using --segment you can look at the regions that are labeled as "different", if you're using --regions I would sort the output file by score and look at the highest scoring regions. Single sites are more difficult to visualize in a holistic way, but maybe generating some plots with summary statistics is a good place to start. It depends a little on what you're experimental objectives are.

saky7009 commented 5 months ago

I got several from Modkit output but do not understand how I can analyze them. saky_output

saky7009 commented 5 months ago

To identify genomic regions with statistically significant differences in DNA methylation patterns between diseased . To study the changes in DNA methylation profiles within targeted gene regions, including promoter regions and CpG islands. These two are my objective