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rather Aarif

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Feb 19, 2024, 5:46:18 AMFeb 19
to HiC-Pro

Hi,

My apologies if this question sounds naive, as I have recently started to learn the pipeline.

I am using the following steps to convert allvalidparis to hic and then to mcool

  1. Merge biological replicates  cat rep1.allValidPairs rep2.allValidPiars > merged.allValidPairs
  2. Run HiCPro
  • ./HiC-Pro_3.1.0/bin/utils/hicpro2juicebox.sh -i merged.allValidPairs -g chromo_sacCer3.sizes -j juicer_tools.2.20.00.ac.jar 
  1. hic2cool convert merged.allValidPairs.hic merged -r 0
  2. cooler balance merged.mcool

I believe that cooler balance merged.mcool. performs the iced normalization

Please correct if if I am wrong, also please help with the full command if I am wrong at any step..

regards

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