Question: How to set 1Kb resolution for Hi-C Juicebox Visualization
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gravatar for harikrishnanc903
2.3 years ago by
harikrishnanc90310 wrote:

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.

chip-seq next-gen • 871 views
ADD COMMENTlink written 2.3 years ago by harikrishnanc90310
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