Question: Overlap CNV with ENCODE DNAse-seq peaks
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gravatar for QVINTVS_FABIVS_MAXIMVS
4.1 years ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.4k wrote:

I have a list of CNVs in BED format and I would like to annotate as likely disrupting accessible DNA regions.

I assume that a naive intersection is not good enough. What are some approaches in annotating genomic positions to DNAse-seq peaks from ENCODE?

Or should I be working with different data, like the BAM files?

cnv dnase-seq encode dnase • 1.0k views
ADD COMMENTlink modified 4.1 years ago by Sinji3.0k • written 4.1 years ago by QVINTVS_FABIVS_MAXIMVS2.4k
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gravatar for Sinji
4.1 years ago by
Sinji3.0k
UT Southwestern Medical Center
Sinji3.0k wrote:

You could possibly use bedtools closest to annotate CNV positions to the nearest DNAse-seq peak.

ADD COMMENTlink written 4.1 years ago by Sinji3.0k
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