Plot

HiFive
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
plotPCA
Function: This tool takes the default output file of multiBamSummary or multiBigwigSummary to perform a principal component analysis (PCA).
Usage: plotPCA [-h] --corData FILE [--plotFile FILE] [--labels sample1 sample2 [sample1 sample2 ...]] [--plotTitle PLOTTITLE] [--plotFileFormat FILETYPE] [--plotHeight PLOTHEIGHT] [--plotWidth PLOTWIDTH] [--outFileNameData file.tab] [--ntop NTOP] [--PCs PCS PCS] [--log2] [--colors COLORS [COLORS ...]] [--markers MARKERS [MARKERS ...]] [--version] [--transpose | --rowCenter]
computeGCBias
Function: This tool computes the GC bias using the method proposed in Benjamini and Speed. The output is used to plot the results and can also be used later on to correct the bias with the tool correctGCbias. There are two plots produced by the tool: a boxplot showing the absolute read numbers per GC-content bin and an x-y plot depicting the ratio of observed/expected reads per GC-content bin.
Usage: computeGCBias -b file.bam --effectiveGenomeSize 2150570000 -g mm9.2bit -l 200 --GCbiasFrequenciesFile freq.txt [options]
HiFive
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
HiFive
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
computeMatrix
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
HiFive
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
HiFive
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
HiFive
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
HiFive
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
HiFive
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
HiFive
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
HiFive
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