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, 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.
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