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.
pip install ${githubpath}
This will set up a command called cooler_ontad in your environment.
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
This tool can be found ready to use in our main container on dockerhub.