Author Topic: finding overlapping regions of CHIP seq BEDs  (Read 3940 times)

cavoli

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finding overlapping regions of CHIP seq BEDs
« on: November 03, 2015, 12:48:39 PM »
Dear All hi,

I am having problems with finding the overlapping regions of chip seq data. with bedops I can find the overlapping regions of multiple chip-seq data. But I cannot implement the peak height of my data to bedops. My genomic locations are important as much as those values.

so my data is consisted of

chr start end peakname value.

Is there a way to implement that value ?

I thought that I can use bedmap for that purpose but I couldnt implement multiple files.

I would be more than glad if you could help me.

Thank your for your help.

Tunc.

AlexReynolds

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Re: finding overlapping regions of CHIP seq BEDs
« Reply #1 on: November 03, 2015, 01:11:39 PM »
You could perhaps take the multiset union of your ChIP-seq datasets:

$ bedops -u chip1.bed chip2.bed ... chipN.bed > chips.bed

Then use chips.bed as the map file in bedmap, applying the --echo-map-score operator to retrieve score (value) data from the unioned dataset:

$ bedmap --echo --echo-map-score --delim '\t' reference_regions.bed chips.bed > reference_regions_with_scores_from_overlapping_chip_peaks.bed

If this does what you want, then you can set up a pipeline to do both steps in one line of code:

$ bedops -u chip1.bed chip2.bed ... chipN.bed | bedmap --echo --echo-map-score --delim '\t' reference_regions.bed - > reference_regions_with_scores_from_overlapping_chip_peaks.bed

This would run faster, since you wouldn't create the intermediate file chips.bed.

I may not fully understand your question, but hopefully this suggests options. Please let us know if this does not help.