Hello, I am currently trying to analyze Hi-C contact matrices. I have been using the Juicer tool https://github.com/aidenlab/juicer/wiki/Data-Extraction and find it very helpful because it contains the Eigen and Pearson command line for extracting correlation matrices and A/B compartment. However, I have read in much of the literature that it is best practice to normalize Hi-C contact matrices, specifically with the popular ICE method https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3816492/.
Juicer provides a few normalization methods (KR, VC, VC_SQRT) however, it does not have an ICE normalization option. I know I could use the dump command to extract matrices, and then pass text matrices through ICE normalization, but after doing this the contact maps will no longer be stored in the aiden labs, .hic file format, and thus I won't be able to easily extract things like Pearson and eigenvalues using the juicer tools jar. Is there a way to easily integrate ICE normalization into the Aiden labs juicer pipeline?