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1. We use the following command to convert the validpairs to hicfile. The 2221-1.allValidPairs is the merged interactions file(~433M)
/home/software/HiC-Pro/HiC-Pro_3.0.0/bin/utils/hicpro2juicebox.sh \
-i /home/HiC/allmerge/2221-1_hicpro/hic_results/data/2221-1/2221-1.allValidPairs \
-g /home/software/HiC-Pro/HiC-Pro_3.0.0/annotation/chrom_mm10.sizes \
-j /home/software/juicer/juicer/scripts/common/juicer_tools.jar \
-r /home/HiC/allmerge/mm10_mboi.bed \
-o ./
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