1 answer
deepTools plotProfile tool does what you want.
Yes, see the usage example on that page. You'll have to run computeMatrix with a bed file containing each of your genes along with bigwigs for your signal.
Have you tried following the examples? Please read the computeMatrix docs closely - you can use a GTF directly.
Hi jared.andrews07 , which bed file shall I used, bed file for the gene (from gtf) or the bed file generated from the macs2 peak calling?
Depends on your question. Are you interested in the signal profile at peaks or at genic regions?
Post your own question if it's more involved than this, piggybacking on old questions is generally discouraged as it makes relevant questions and answers harder to find for people.
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