OnTAD for coolers

cooler_ontad is a tool that wraps OnTAD to work with the cooler ecosystem.

This tool consists of three steps:

• It creates a dense matrix for OnTAD out of a .mcooler file,
• runs OnTAD,
• and creates a .bedpe out of the ONTAD results, all parameters used will be extended to the filename.

Install with pip:

pip install ${githubpath}

This will set up a command called cooler_ontad in your environment.

Usage Examples:

Example files can be found on GEO. You will need to zoomify .cooler to .mcooler first.

This will show all possible options, the tools support all options of OnTAD:

cooler_ontad --help

This will run with the default parameters:

cooler_ontad --binsize testdata/G2.fc_1_2.cis.1000.mcool

This will run with the binsize reduced to 30000 and only add non default parameters to the filname:

cooler_ontad --shortname --binsize 30000 testdata/G2.fc_1_2.wOldG2.cis.1000.mcool

Dockerhub container:

This tool can be found ready to use in our main container on dockerhub.