Question: Overlap CNV with ENCODE DNAse-seq peaks
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gravatar for QVINTVS_FABIVS_MAXIMVS
3.2 years ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.3k 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 • 870 views
ADD COMMENTlink modified 3.2 years ago by Sinji2.8k • written 3.2 years ago by QVINTVS_FABIVS_MAXIMVS2.3k
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gravatar for Sinji
3.2 years ago by
Sinji2.8k
UT Southwestern Medical Center
Sinji2.8k wrote:

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

ADD COMMENTlink written 3.2 years ago by Sinji2.8k
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