Any one knows any command line tools/methods/scripts to calculate correlation coefficient from two BED files of two ChIP-seq replicates?
thanks
thanks
-
-
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
-
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment