Plot Venn diagram given two bed files

Please use intervene [here](https://intervene.readthedocs.io/en/latest/examples.html)

hpcf_interactive

source activate /home/yli11/.conda/envs/py2

module load R/3.5.1

intervene upset -i *unmatched.realign.tsv

Result is stored in a folder called Intervene_results

OLD notes

usage: bed2venn.py [-h] -b1 B1 -b2 B2 -l1 L1 -l2 L2 [-e1 E1] [-e2 E2]
                   [--fontsize FONTSIZE] [-o OUTPUT]

optional arguments:
  -h, --help            show this help message and exit
  -b1 B1                bed file 1 (default: None)
  -b2 B2                bed file 2 (default: None)
  -l1 L1                label 1 (default: None)
  -l2 L2                label 2 (default: None)
  -e1 E1                extend b1 bed file by e1 bp (default: None)
  -e2 E2                extend b2 bed file by e2 bp (default: None)
  --fontsize FONTSIZE   label 2 (default: 10)
  -o OUTPUT, --output OUTPUT
                        output file name (default: yli11_2021-04-26)

Summary

This program will calculate the amount of overlaps given two bed files.

Note that, it is very likely that the number of A overlapping with B is different than the number of B overlapping with A.

For example, let’s say A is an entire chromosome, B is some scattered regions in this chromosome. Then, the number of A overlapping with B is 1 and the number of B overlapping with A is |B|.

Input

Two bed files. Any bed formats that are supported by bedtools are acceptable here. e.g., narrowpeak files.

Output

Usage

hpcf_interactive

module load python/2.7.13

bed2venn.py -b1 bed1 -b2 bed2 -l1 treatment -l2 control

To extend Xbp left and right on -b1 bed file or -b2 bed file, please use -e1 or -e2

hpcf_interactive

module load python/2.7.13

bed2venn.py -b1 bed1 -b2 bed2 -l1 treatment -l2 control -e1 5000

code @ github.