| HiFive |
hifive hic-normalize <SUBCOMMAND> [-h] [-m MINDIST] [-x MAXDIST] [-c CHROMS] [-o OUTPUT] [-q] [normalization options] project |
Find correction parameter values using one of the available algorithms. |
| computeMatrix |
computeMatrix reference-point -S <biwig file> -R <bed file> -a 3000 -b 3000 |
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. |
| HiFive |
hifive fragments [-h] [-r RE] [-g GENOME] [-q] bed output |
Create a fragment file from a BED file containing targeted RE fragment data. |
| HiFive |
hifive fends [-h] (-F FEND | -B BED | -L LENGTH) [--binned] [-r RE] [-g GENOME] [-q] output |
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. |
| HiFive |
hifive hic-combine-replicates [-h] [-q] replicate1 replicate2 output |
Combine multiple HiC data files into a single file without needing to reload the data. |
| plotPCA |
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] |
This tool takes the default output file of multiBamSummary or multiBigwigSummary to perform a principal component analysis (PCA). |
| HiFive |
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 |
Using an already created HiC project, generate an HDF5-formatted heatmap file and optional image. |
| HiFive |
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 |
Using an already created HiC project, generate a tabular genomic-interval or matrix file for a specified region and optional image. |