How to check a gene in an open chromatin region or not?

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19 months ago

Chris ▴ 340

Hi all, I try to check if my gene of interest is in an open chromatin region or not so I think I could use ucsc genome browser. But that site is quite complicated so I am not sure where to put my bam files to able to see the peaks. I got a suggestion: go to My data then track hubs but I am not sure. Would you have a suggestion? Thank you!

ATAC-seq • 917 views

ADD COMMENT • link 18 months ago by Chris ▴ 340

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Use the Integrated Genome Viewer. Make a bigwig file out of the bam first, using for example deeptools bamCoverage with a binsize of 1.

ADD REPLY • link 19 months ago by ATpoint 85k

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Thanks ATpoint! Will check it and let you know soon.

ADD REPLY • link 19 months ago by Chris ▴ 340

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I open igv_session.xml on Integrated Genome Viewer and got this:

enter image description here

Is that what I should look for to find the gene of interest? I still trying to interpret this plot as a beginner in ATAC seq.

ADD REPLY • link 19 months ago by Chris ▴ 340

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Read IGV manual. You can enter gene names in that field on top, but you also have to scale the tracks.

ADD REPLY • link 19 months ago by ATpoint 85k

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When I enter the gene symbol into the search box, I got: cannot find feature or locus: ABC gene. Would you please have a suggestion?
Update: I figured it out.

ADD REPLY • link 18 months ago by Chris ▴ 340

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