what is the lowest computer set up for hicBuildmatrix?

Question

[foxjuly]

Hi, does anyone know what is the lowest setup for running hicBuildmarix? I am currently trying to analyze some of the data published by other groups in 4DN portal. I found hicBuildmatrix is quite memory demanding and will gradually eat up all internal memories. typically, I want to build matrix from two .bam file created by bwa mem, which each takes ~10 GB space.I then run hicBuildMatrix with bin set to 10000 (for human genome it's ~300 kb resolution). I found I gradually run out of memory and failed eventually. So, could anyone give some suggestions. I currently don't have access to HPC. Thanks a lot!

Answer 1

[wolffj.bioinf]

Hi,

I would recommend at least 32 GB of memory to build a Hi-C interaction matrix, you can set the number of used cores to 2 to decrease memory usage.

Concerning too less resources: We offer https://hicexplorer.usegalaxy.eu with a limit of 250 GB of HDD space but no RAM or CPU limitations. Feel free to register an account on our server.

Best,

Joachim