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Function: HiFive is a tool for handling, normalizing, and plotting HiC and 5C chromatin interaction data. This command performs all of the steps of the subcommands fragments, 5c-data, 5c-project, and 5c-normalization in one command.
Usage: hifive 5c-complete <SUBCOMMAND> [-h] [-r RE] [-g GENOME] (-B BAM BAM | -C COUNT) [-f MININT] [-m MINDIST] [-x MAXDIST] [-r REGIONS] (-o OUTPUT OUTPUT OUTPUT | -P PREFIX) [-q] [normalization options] bed
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Function: Using an already created 5C project, generate a tabular genomic-interval file for a specified region and optional image.
Usage: hifive 5c-interval [-h] -c REGION [-s START] [-e STOP] [--region2 REGION2] [--start2 START2] [--stop2 STOP2] [-b BINSIZE] [-d {raw,fragment,distance,enrichment,expected}] [-y] [-x EXPBINSIZE] [-f MINOBS] [-g SEARCH] [-v] [-i IMAGE] [-p] [-r] [-t] [-l] [-k KEYWORDS] [-q] project output
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Function: Create a project file, filter fragments, and estimate distance-dependence.
Usage: hifive 5c-project [-h] [-f MININT] [-m MINDIST] [-x MAXDIST] [-q] data output
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Function: This tool prepares an intermediate file (a gzipped table of values) that contains scores associated with genomic regions. The regions can either be scaled to the same size (using the scale-regions mode) or you can choose the start, end, or center of each region as the focus point for the score calculations.
Usage: computeMatrix reference-point -S <biwig file> -R <bed file> -a 3000 -b 3000
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Function: Create a project file, filter fends, and estimate distance-dependence.
Usage: hifive hic-project [-h] [-f MININT] [-m MINDIST] [-x MAXDIST] [-j MINBIN] [-n NUMBINS] [-q] data output
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Function: Create a data file from mapped BAM, MAT, or paired coordinate text (RAW) files or from binned matrix files.
Usage: hifive hic-data [-h] (-S BAM BAM | -R RAW | -M MAT | -X MATRIX) [-i INSERT] [--skip-duplicate-filtering] [-q] fend output
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Function: Create a multi-resolution heatmap file from a HiFive HiC project file.
Usage: hifive hic-mrheatmap [-h] [-t] [-c CHROMS] [-f MINOBS] [-B MAXBIN] [-b MINBIN] [-R MAXTRANSBIN] [-r MINTRANSBIN] [-m MIDBIN] [-d {raw,fend,distance,enrichment}] [-q] project output
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Function: Combine multiple HiC data files into a single file without needing to reload the data.
Usage: hifive hic-combine-replicates [-h] [-q] replicate1 replicate2 output
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Function: Find correction parameter values using one of the available algorithms.
Usage: hifive hic-normalize <SUBCOMMAND> [-h] [-m MINDIST] [-x MAXDIST] [-c CHROMS] [-o OUTPUT] [-q] [normalization options] project
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Function: Create a fragment file from a BED file containing targeted RE fragment data.
Usage: hifive fragments [-h] [-r RE] [-g GENOME] [-q] bed output
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Function: Create a fend file from either a BED or HiCPipe-style fend file containing RE fragment data or create an arbitrarily-binned interval file from chromosome length file.
Usage: hifive fends [-h] (-F FEND | -B BED | -L LENGTH) [--binned] [-r RE] [-g GENOME] [-q] output
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Function: Using an already created HiC project, generate an HDF5-formatted heatmap file and optional image.
Usage: hifive hic-heatmap [-h] [-b BINSIZE] [-t] [-c CHROMS] [-d {raw,fend,distance,enrichment,expected}] [-F {hdf5,txt,npz}] [-y] [-x EXPBINSIZE] [-f MINOBS] [-a SEARCH] [-v] [-i IMAGE] [-p] [-l] [-n] [-k KEYWORDS] [-q] project output
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Function: Using an already created HiC project, generate a tabular genomic-interval or matrix file for a specified region and optional image.
Usage: hifive hic-interval [-h] -c CHROM [-s START] [-e STOP] [-b BINSIZE] [-m MAXDIST] [-d {raw,fend,distance,enrichment,expected}] [-M] [-y] [-x EXPBINSIZE] [-f MINOBS] [-a SEARCH] [-v] [-i IMAGE] [-p] [-r] [-t] [-l] [-k KEYWORDS] [-q] project output