ChromHMM bed file annotation
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12 weeks ago
SEJAL • 0

I used chromHMM to get different states/segments. My output file is the bed file. I want to annotate it and see which genes lie in a particular state based on the distance from TSS. How can it be done?

Chromhmm annotation • 318 views
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By bedtools intersect (https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html ) with a second BED that contains the relevant annotations.

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I want to get the genes which fall in these segments, my segments are active promoter regions and I need the genes whose promoters fall in these active promoter regions

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