BED intersects/overlaps output for Venn diagrams - single column

Question

[rbronste]

Kind of a basic question, but is there a way to represent the output of intersects or dropouts via single columns in a list so as to facilitate making a venn diagram after. Specifically if you have several BED files. Thanks.

Answer 1

[Alex Reynolds]

BEDOPS works with standard input and output streams, so you can pipe results to standard Unix tools. You can pipe the result to cut with awk to count, or pipe to wc -l to count lines. If you're using bedmap, you can use --countto count mapped elements.

Answer 2

[esimonova.me]

Try intervene module to visualize it (https://intervene.readthedocs.io/en/latest/modules.html):

intervene venn -i path/to/BED/files/*.bed --output ~/results/path