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>:
{venn,upset,pairwise}
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 https://github.com/asntech/intervene/tree/master/intervene/example_data 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