how to get methylated fragments (CpG regions) for only ONE sample using DMAP

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4.2 years ago

maria2019 ▴ 250

Hi,

I am trying to count CpG regions in one of my samples. I know that I can find DMR using DMAP/diffmeth (below is my code). How ever, I do not know how to find (and count) methylated fragments in only one sample. Any suggestions?

diffmeth -G $ref_path -A 40,220 -U 0.05 -N -I 5 -R $sample1 -R $sample2 -S $sample3 -S $sample4

In fact, I need to get a result like TABLE 1 in the DMAP paper (https://academic.oup.com/bioinformatics/article/30/13/1814/2422202), but could not find the script to generate such data.

Dmap DMR methylation CpG • 859 views

ADD COMMENT • link updated 2.3 years ago by iraia.munoa ▴ 130 • written 4.2 years ago by maria2019 ▴ 250

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Hi! Did you find the pipeline to follow for the DMAP tool? I am in the same situation as you, when trying to use it. Did you finally find any other tool easy to use? Thanks!!

ADD REPLY • link 2.3 years ago by iraia.munoa ▴ 130

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