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vaquerizaslab / chess

Comparison of Hi-C Experiments using Structural Similarity.
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Normalization of .hic files #62

Open aminakur opened 1 year ago

aminakur commented 1 year ago

I have two unbalanced .hic files generated by Juicer. I used chess-sim with the following command:

chess sim --background-query -p 24 /az_new/az_new.hic@2000@KR \
    /NPB_new/NPB_new.hic@2000@KR \
    az_npb_SBs.bedpe az_npb_syntenic_2kb.tsv

Dies the @KR work in this code? Would it compare the normalized matrices as a result?

kaukrise commented 1 year ago

CHESS uses FAN-C to load Juicer matrices, so yes, the command above should compare KR-normalised 2kb resolution matrices.