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  • Correlation Coefficient between ChIP-seq replicates

    Any one knows any command line tools/methods/scripts to calculate correlation coefficient from two BED files of two ChIP-seq replicates?

    thanks

  • #2
    Get peaks from your bed files (macs14 or macs2)......intersectBed (to find the overlapping peaks)....output to a text file.....import into R.....run your correlation coefficient on the scores (from the macs peak caller). I can give you more details if you need it.

    One negative is that intersectBed tosses out situations where one feature is present and one feature isn't. Well, not exactly...you can keep the "zeros" from one sample, but not from both. I had to write my own script to deal with that issue.

    Or just check the "similar threads" above your original post....http://seqanswers.com/forums/showthr...t=19099....for a solution that uses the raw-ish reads.

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    • #3
      Hi
      Would you please give me some detail about calculating the PCC on R?
      I did peak calling by Sicer and then I find overlap by intersectsBED. but I do not know how to fin Pearson correlation

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