I don't think there is an official way of converting.
hic, the other way around is supported by hic2cool. I agree that it is not easy to setup but it is worth the troubles.įor. You can load your mcool files in your own HiGlass server that you can launch on your local machine using higlass-manage as explained in their documentation: The -r flag here specifies the resolutions you would like your. Where the chrom.sizes file contains two columns. So that converting the short format with score file is done with the following: However, you may need to increase the resourced allocated to the JVM for very large files:Īlias juicer='java -Xms512m -Xmx2048m -jar path/to/juicer_tools_1.22.01.jar' I downloaded juicer tools from here: and set the following alias. Sometimes this file will need to be sorted as juicer requires a specific chromosome ordering. hic anyway) and made sure that the dummy variables for frag1 and frag2 were different, using the following awk command:Īwk -F "\t" '' >
The ginteractions file does not contain fragment or strand information, so I put dummy variables for those (since they are not used for the conversion to. I opted to make the file into short format with score, which has columns like: Documentation on the input formats accepted can be found here. Next, we will do some format preparation on this file to make it compatible with juicer pre. HicConvertFormat -m /path/to/ol -o /path/to/file.ginteractions -inputFormat cool -outputFormat ginteractions hicįirstly, use the hicConvertFormat tool from the HiCExplorer package (which I installed using conda) to convert your. I've put together a slightly hacky and long winded way to go from.
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