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Any one knows any command line tools/methods/scripts to calculate correlation coefficient from two BED files of two ChIP-seq replicates?
thanks
thanks
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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. -
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 correlationComment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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