Question: how to compare two TF binding sites
1
gravatar for mikysyc2016
2.5 years ago by
mikysyc201680
mikysyc201680 wrote:

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!

chip-seq • 852 views
ADD COMMENTlink written 2.5 years ago by mikysyc201680
1

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.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Arup Ghosh2.7k
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Bioconductor's GenomicRanges package has numerous functions to compute overlaps between sets of genomic ranges (e.g. ChIP-seq peaks)

ADD REPLYlink written 2.5 years ago by ejm32440
1

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

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Bioinformatist Newbie250

Thank you for your nice reply!

ADD REPLYlink written 2.4 years ago by mikysyc201680
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