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Overlap CNV with ENCODE DNAse-seq peaks

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 dnase encode
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updated by Sinji Sinji • written by QVINTVS_FABIVS_MAXIMVS QVINTVS_FABIVS_MAXIMVS

1 answer

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

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written by Sinji Sinji

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