How to use Intervene

Once you have installed Intervene, you can type:

intervene --help

This will show the main help, which lists the three subcommands/modules: venn, upset, and pairwise.

usage: intervene <subcommand> [options]

positional arguments <subcommand>:
                        List of subcommands
    venn                Venn diagram of intersection of genomic regions or list sets (upto 6-way).
    upset               UpSet diagram of intersection of genomic regions or list sets.
    pairwise            Pairwise intersection and heatmap of N genomic region sets in <BED/GTF/GFF> format.

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit

To view the help for the individual subcommands, please type:

To view venn module help, type

intervene venn --help

To view upset module help, type

intervene upset --help

To view pairwise module help, type

intervene pairwise --help

Run Intervene on test data

To run Intervene using example data, use the following commands. To access the test data make sure you have sudo or root access.

To run venn module with test data, type

intervene venn --test

To run upset module with test data, type

intervene upset --test

To run pairwise module with test data, type

intervene pairwise --test

If you have installed Intervene locally from the source code, you may have problem to find test data. You can download the test data here and point to it using -i instead of --test.

./intervene/intervene venn -i intervene/example_data/ENCODE_hESC/*.bed
./intervene/intervene upset -i intervene/example_data/ENCODE_hESC/*.bed
./intervene/intervene pairwise -i intervene/example_data/dbSUPER_mm9/*.bed

These subcommands will save the results in the current working directory with a folder named Intervene_results. If you wish to save the results in a specific folder, you can type:

intervene <module_name> --test --output ~/path/to/your/results/folder