how to compare two TF binding sites

Question

[mikysyc2016]

Hi all, I have two questions: 1.I do ChIP-seq for two different tanscription factors in sample sample and want to compare their overlap binding sites and individual binding sites. 2.I want to cmpare same TF binding sites in different samples( like wt and ko). Could you recommend some useful software? Thanks!

[Arup Ghosh]

If you are planning to overlap multiple ChIP-seq region files and want all the overlapping and unique regions you can use BedSect. It utilizes Bedtools multiIntersectBed for the multiplicity calculation and provides each possible overlap (with region coordinates) combination as output.

[ejm32]

Bioconductor's GenomicRanges package has numerous functions to compute overlaps between sets of genomic ranges (e.g. ChIP-seq peaks)

[Bioinformatist Newbie]

If you have peak files for respective TFs and conditions, you can use Bedtools intersect to get what you want.

1a: For overlap binding sites: bedtools intersect -a TF1.peakFile -b TF2.peakFile > overlappingSites.bed

1b: For individual binding sites: bedtools intersect -a TF1.peakFile -b TF2.peakFile -v > uniqueTF1.bed

Similarly, you can do it for the same TF peak files in 2 different conditions as well: bedtools intersect -a TF1_WT.peakFile -b TF1_KO.peakFile > overlappingSites.bed

[mikysyc2016]

Thank you for your nice reply!