I am currently running HiC-spector on mouse genome datasets with bin size 5kb. I noticed that it requires quite a lot of memory, so I was wondering if there were tests done on HiC-spector’s space complexity, as I couldn’t find such studies in the Supplementary Data.
We didn’t do analysis explicitly. Because the contact maps are stored as sparse matrices, the memory won’t grow quadratically. In general, if calculation is done chromosome by chromosome, 5kb should be fine.