Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Pearson correlation between replicates afreund Bioinformatics 9 06-05-2014 01:38 AM
ChIP-seq peak calling from replicates ttnguyen Bioinformatics 4 08-10-2011 02:21 AM
ChIP-Seq Biological Replicates LouDore General 0 08-11-2009 12:35 PM
some questions about ChIP-Seq replicates/controls hongyan Epigenetics 3 09-24-2008 01:07 PM

Thread Tools
Old 07-26-2012, 02:45 AM   #1
Junior Member
Location: Africa

Join Date: Nov 2009
Posts: 5
Default 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?

abmmki is offline   Reply With Quote
Old 07-26-2012, 02:11 PM   #2
Junior Member
Location: MD

Join Date: Jul 2011
Posts: 9

Get peaks from your bed files (macs14 or macs2)......intersectBed (to find the overlapping peaks)....output to a text file.....import into 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 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.... a solution that uses the raw-ish reads.
thedavid is offline   Reply With Quote
Old 12-29-2016, 09:59 AM   #3
Junior Member
Location: US

Join Date: Dec 2016
Posts: 1

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
mforo01 is offline   Reply With Quote

chip-seq pcc count-data

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 08:20 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO