I am just getting started analyzing Hi-C data to call TADs. It seems that there is not yet a consensus on which software tools are best to make an analysis pipeline. I have so far tried Hicup (from Babraham) for alignments, homer for making heatmaps and have been trying to install Juicer which offers a full pipeline.
I am wondering if anyone has any advice on which software tools they use in their analysis workflow. I would be particularly interested advice as to which is the best TAD caller to use.
Thanks for your help!