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vaquerizaslab / chess

Comparison of Hi-C Experiments using Structural Similarity.
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speed up the chess run #51

Closed zy041225 closed 2 years ago

zy041225 commented 3 years ago

Dear all,

Thank you for providing this tool. But I'm wondering if it is possible to speed up the chess run. I'm suffering from the slow chess sim process. It takes more than 4 days to read a primate reference balanced cool file. The cool file is in 20Kb resolution generated from ~30X Hi-C reads, about 2Gb in size. Since I'm only interested in one particular chromosome, is it possible to generate a subset of the data as input for chess?

Many thanks

Best, Yang

liz-is commented 3 years ago

Hello, Yes, you can certainly use a Hi-C file that has been subsetted to only contain your chromosome of interest. You might also consider converting your .cool file to Juicer or FAN-C format, see here: https://chess-hic.readthedocs.io/en/latest/faq.html#why-is-chess-sim-so-slow