Hic juicebox full#
GW_KR) Full list of built-in normalizations is VC, VC_SQRT, KR,SCALE, GW_KR, GW_SCALE, GW_VC, INTER_KR, INTER_SCALE, INTER_VC -k calculate specific normalizations (including genomewide normalizations, e.g.-g Add the text graphs file to the Hi-C file header.-s Add the text statistics file to the Hi-C file header.-t Set a temporary directory for writing.-r Only calculate specific resolutions.-c Only calculate map on specific chromosome.-q Filter by MAPQ score greater than or equal to q.-m Only write cells with count above threshold m.Position of each restriction site on that chromosome, in numeric order, andĮnding with the size of the chromosome Requires restriction siteįile each line should start with the chromosome name followed by the -d Only calculate intra chromosome (diagonal).SusScr3, or TAIR10 alternatively, this can be the path of the chrom.sizes file that lists on each line the name and size of the chromosomes. : Must be one of hg18, hg19, hg38, dMel, mm9, mm10, anasPlat1,īTaurus3, canFam3, equCab2, galGal4, Pf3D7, sacCer3, sCerS288c,.Load into Juicebox or operate on using Juicebox tools. The text file should be in one of the formats below. It takes three required arguments and a number of optional arguments. If the user sends in a restriction site file, an additional 8 fragment-delimited resolutions are added: 500f, 250f, 100f, 50f, 20f, 5f, 2f, 1f. hic files are created from a text file describing the Hi-C reads and bin the reads at 9 base-pair-delimited resolutions: 2.5M, 1M, 500K, 250K, 100K, 50K, 25K, 10K, and 5K.
hic file, a highly compressed binary file that provides rapid random access to the matrices.hic files can be visualized in the Juicebox GUI and data can be easily extracted from them using the dump command our sophisticated feature annotation algorithms also operate on. The Juicer Tools and Juicebox software is centered around the.
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