Open ratheraarif opened 4 months ago
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
cat rep1.allValidPairs rep2.allValidPiars > merged.allValidPairs
./HiC-Pro_3.1.0/bin/utils/hicpro2juicebox.sh -i merged.allValidPairs -g chromo_sacCer3.sizes -j juicer_tools.2.20.00.ac.jar
hic2cool convert merged.allValidPairs.hic merged -r 0
cooler balance merged.mcool
I believe that cooler balance merged.mcool. performs the iced normalization
cooler balance merged.mcool.
Please correct if if I am wrong, also please help with the full command if I am wrong at any step..
regards
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
cat rep1.allValidPairs rep2.allValidPiars > merged.allValidPairs./HiC-Pro_3.1.0/bin/utils/hicpro2juicebox.sh -i merged.allValidPairs -g chromo_sacCer3.sizes -j juicer_tools.2.20.00.ac.jarhic2cool convert merged.allValidPairs.hic merged -r 0cooler balance merged.mcoolI believe that
cooler balance merged.mcool.performs the iced normalizationPlease correct if if I am wrong, also please help with the full command if I am wrong at any step..
regards