HiC-spector space complexity

Q:
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.

A:
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.

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