A lot of tools are present for Hi-C data analysis, some these include HiCCUPs, diffHiC. Fit-HiC, mHiC, hicexplorer, HiPPIE etc.
My question is regarding Hi-C data analysis associated with plant genomes. In plant genomes we encounter polyploidy and repeats. This also results in handling of multimapping reads.
If you have experience in the field, what would be your suggestion for the computational tool.
Starting from the aligner and your setting for it.
Thank you in advance.