Do peaks overlap across samples? Let's find out, using find_overlaps function (John Rinn Teaching)

Now that we know how to import peak files, let's learn new skills to find how ATACseq peaks overlap between samples (replicates). This will identify which peaks were found in both replicates for a given time point. That means they are reproducible across replicates - a great thing to find.

Finding overlaps of "GRanges" data is VERY common so we will build a function so you can do these analyses faster - and we can find ATACseq peaks that are present in all of our samples too !

Let's go find overlaps of ATACseq peaks across samples !

The data for this lesson is here ( the .broadPeak files):
Mouse .broadPeak files for this specific lesson - but same thing can be applied to any other ATACseq output peak files.

Needed peak files are here:
https://rinnformatics.colorado.edu/mo...

Genome annotation file can be downloaded here:
https://rinnformatics.colorado.edu/ge...

John Rinn Github for this class:
https://github.com/boulderrinnlab/MAS...

John Rinn CGL Website for this class:
https://www.lncrna.io/cgl-level-9

-ATACseq OUTPUT FILES HERE:
https://rinnformatics.colorado.edu/mo...

John Rinn BioFrontiers:
https://www.colorado.edu/biofrontiers...

John Rinn Lab:
http://www.lncRNA.io

John Rinn Teaching:
http://www.lncrna.io/teaching

John Rinn University of Colorado Boulder Biochemistry:
https://www.colorado.edu/biochemistry...

John Rinn Linkedin:
  / john-rinn  

#johnrinn
#ATACseq
#iranges
#granges