I am using Homer tool to identify contact matrix in the genome. For visualization of contact matrics, I am using Juicebox. Using pre I have created Hi-C file from maketagdirectory. In Jucier tool the pre-command bin the reads at 9 base-pair-delimited resolutions: 2.5M, 1M, 500K, 250K, 100K, 50K, 25K, 10K, and 5K. I need to bin the reads at 1kb resolution. If anybody is an expert in this area kindly provide help. I have used the following command
tagDir2hicFile.pl HiC_tag/ -juicerOpt "-r 5000,1000" -juicer auto -genome hg19 -p 30
tagDir2hicFile.pl in homer create *.hic files from maketagdirectory. The Perl code uses pre-command from Juicer tool to create Hi-C file.