Chip-Seq Analysis: How To Pair Plus And Minus Strand Peaks

Question

[Ashutosh]

After peak calling with GeneTrack, how to pair plus and minus strand peaks if peaks are on 3' end to each other & < 100 bp apart. I also want to know, how to normalize ChIP-exo data such that total tag count inside of background regions are same. background regions are defined as any region that lacks a peak pair within 100 bp.

Answer 1

[Istvan Albert]

You can use bedtools to perform various kinds of interval operations.

Answer 2

[dnaseiseq]

CexoR: An R/Bioconductor package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates