Function: This tool creates a heatmap for scores associated with genomic regions. The program requires a matrix file generated by the tool computeMatrix
Usage: plotHeatmap [--matrixFile MATRIXFILE] --outFileName OUTFILENAME [--outFileSortedRegions FILE] [--outFileNameMatrix FILE] [--interpolationMethod STR] [--dpi DPI] [--kmeans KMEANS] [--hclust HCLUST] [--silhouette] [--help] [--version] [--plotType {lines,fill,se,std}] [--sortRegions {descend,ascend,no,keep}] [--sortUsing {mean,median,max,min,sum,region_length}] [--sortUsingSamples SORTUSINGSAMPLES [SORTUSINGSAMPLES ...]] [--linesAtTickMarks] [--clusterUsingSamples CLUSTERUSINGSAMPLES [CLUSTERUSINGSAMPLES ...]] [--averageTypeSummaryPlot {mean,median,min,max,std,sum}] [--missingDataColor MISSINGDATACOLOR] [--colorMap COLORMAP [COLORMAP ...]] [--alpha ALPHA] [--colorList COLORLIST [COLORLIST ...]] [--colorNumber COLORNUMBER] [--zMin ZMIN [ZMIN ...]] [--zMax ZMAX [ZMAX ...]] [--heatmapHeight HEATMAPHEIGHT] [--heatmapWidth HEATMAPWIDTH] [--whatToShow {plot, heatmap and colorbar,plot and heatmap,heatmap only,heatmap and colorbar}] [--boxAroundHeatmaps BOXAROUNDHEATMAPS] [--xAxisLabel XAXISLABEL] [--startLabel STARTLABEL] [--endLabel ENDLABEL] [--refPointLabel REFPOINTLABEL] [--labelRotation LABEL_ROTATION] [--regionsLabel REGIONSLABEL [REGIONSLABEL ...]] [--samplesLabel SAMPLESLABEL [SAMPLESLABEL ...]] [--plotTitle PLOTTITLE] [--yAxisLabel YAXISLABEL] [--yMin YMIN [YMIN ...]] [--yMax YMAX [YMAX ...]] [--legendLocation {best,upper-right,upper-left,upper-center,lower-left,lower-right,lower-center,center,center-left,center-right,none}] [--perGroup] [--plotFileFormat] [--verbose]
Function: Compute the average scores for each of the bigWig files in certain user selected regions (e.g. genes).
Usage: multiBigwigSummary BED-file -b -out results.npz --BED selection.bed
Function: This tool creates a profile plot for scores over sets of genomic regions. Typically, these regions are genes, but any other regions defined in BED will work. A matrix generated by computeMatrix is required.
Usage: plotProfile [--matrixFile MATRIXFILE] --outFileName OUTFILENAME [--outFileSortedRegions FILE] [--outFileNameData OUTFILENAMEDATA] [--dpi DPI] [--kmeans KMEANS] [--hclust HCLUST] [--silhouette] [--help] [--version] [--averageType {mean,median,min,max,std,sum}] [--plotHeight PLOTHEIGHT] [--plotWidth PLOTWIDTH] [--plotType {lines,fill,se,std,overlapped_lines,heatmap}] [--colors COLORS [COLORS ...]] [--numPlotsPerRow NUMPLOTSPERROW] [--clusterUsingSamples CLUSTERUSINGSAMPLES [CLUSTERUSINGSAMPLES ...]] [--startLabel STARTLABEL] [--endLabel ENDLABEL] [--refPointLabel REFPOINTLABEL] [--labelRotation LABEL_ROTATION] [--regionsLabel REGIONSLABEL [REGIONSLABEL ...]] [--samplesLabel SAMPLESLABEL [SAMPLESLABEL ...]] [--plotTitle PLOTTITLE] [--yAxisLabel YAXISLABEL] [--yMin YMIN [YMIN ...]] [--yMax YMAX [YMAX ...]] [--legendLocation {best,upper-right,upper-left,upper-center,lower-left,lower-right,lower-center,center,center-left,center-right,none}] [--perGroup] [--plotFileFormat] [--verbose]
Function: This tool computes and visualizes the pairwise correlation among samples as scatterplots or as a heatmap. It works with the outputs generated by multiBamSummary or multiBigwigSummary.
Usage: plotCorrelation [options] --corData FILE --corMethod {spearman,pearson} --whatToPlot {heatmap,scatterplot}
Function: This tool determines read/fragment coverage of regions. The regions (e.g., exons, genes or peaks) can be specified in one or more BED or GTF files. For GTF files, the feature type is taken from column 3. For BED files, the file name is used. For BED files, the feature labels can be changed.
Usage: plotEnrichment [-h] --bamfiles file1.bam file2.bam [file1.bam file2.bam ...] --BED FILE1.bed FILE2.bed [FILE1.bed FILE2.bed ...] [--plotFile FILE] [--attributeKey ATTRIBUTEKEY] [--labels sample1 sample2 [sample1 sample2 ...]] [--smartLabels] [--regionLabels region1 region2 [region1 region2 ...]] [--plotTitle PLOTTITLE] [--plotFileFormat FILETYPE] [--outRawCounts FILE] [--perSample] [--variableScales] [--plotHeight PLOTHEIGHT] [--plotWidth PLOTWIDTH] [--colors COLORS [COLORS ...]] [--numPlotsPerRow NUMPLOTSPERROW] [--alpha ALPHA] [--Offset INT [INT ...]] [--keepExons] [--version] [--region CHR:START:END] [--blackListFileName BED file [BED file ...]] [--numberOfProcessors INT] [--verbose] [--extendReads [INT bp]] [--ignoreDuplicates] [--minMappingQuality INT] [--centerReads] [--samFlagInclude INT] [--samFlagExclude INT] [--minFragmentLength INT] [--maxFragmentLength INT]
Function: This tool is useful to assess the sequencing depth of a given sample. It samples 1 million bp, counts the number of overlapping reads and can report a histogram that tells you how many bases are covered how many times. Multiple BAM files are accepted, but they all should correspond to the same genome assembly.
Usage: plotCoverage --bamfiles FILE1 FILE2 [FILE1 FILE2 ...] [--help] [--plotFile PLOTFILE] [--labels sample1 sample2 [sample1 sample2 ...]] [--smartLabels] [--plotTitle PLOTTITLE] [--skipZeros] [--numberOfSamples NUMBEROFSAMPLES] [--BED FILE1.bed FILE2.bed [FILE1.bed FILE2.bed ...]] [--outRawCounts FILE] [--outCoverageMetrics FILE] [--coverageThresholds COVERAGETHRESHOLDS] [--plotHeight PLOTHEIGHT] [--plotWidth PLOTWIDTH] [--plotFileFormat FILETYPE] [--region CHR:START:END] [--blackListFileName BED file [BED file ...]] [--numberOfProcessors INT] [--verbose] [--extendReads [INT bp]] [--ignoreDuplicates] [--minMappingQuality INT] [--centerReads] [--samFlagInclude INT] [--samFlagExclude INT] [--minFragmentLength INT] [--maxFragmentLength INT] [--version]
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 scale-regions -S <biwig file> -R <bed file> -b 1000
Function: This tool samples indexed BAM files and plots a profile of cumulative read coverages for each. All reads overlapping a window (bin) of the specified length are counted; these counts are sorted and the cumulative sum is finally plotted.
Usage: plotFingerprint -b treatment.bam control.bam -plot fingerprint.png
Function: Find correction parameter values using one of the available algorithms.
Usage: hifive 5c-normalize <SUBCOMMAND> [-h] [-m MINDIST] [-x MAXDIST] [-r REGIONS] [-o OUTPUT] [-q] [normalization options] project
Function: Create a data file from mapped BAM or fragment-pair counts files.
Usage: hifive 5c-data [-h] (-B BAM BAM | -C COUNT) [-q] fragment output
Function: Using an already created 5C project, generate an HDF5-formatted heatmap file and optional image.
Usage: hifive 5c-heatmap [-h] [-b BINSIZE] [-t] [-r REGIONS] [-d {raw,fragment,distance,enrichment,expected}] [-a {compact,full}] [-y] [-x EXPBINSIZE] [-f MINOBS] [-g SEARCH] [-v] [-i IMAGE] [-p] [-l] [-n] [-k KEYWORDS] [-q] project output
Function: Perform all of the steps of the subcommands fends, hic-data, hic-project, and hic-normalization in one command.
Usage: hifive hic-complete <SUBCOMMAND> [-h] (-F FEND | -B BED | -L LENGTH) [--binned] [-r RE] [-g GENOME] (-S BAM BAM | -R RAW | -M MAT | -X matrix) [-i INSERT] [--skip-duplicate-filtering] [-f MININT] [-m MINDIST] [-x MAXDIST] [-j MINBIN] [-n NUMBINS] [-c CHROMS] (-o OUTPUT OUTPUT OUTPUT | -P PREFIX) [-q] [normalization options]
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] [--ntop NTOP] [--PCs PCS PCS] [--log2] [--colors COLORS [COLORS ...]] [--markers MARKERS [MARKERS ...]] [--version] [--transpose | --rowCenter]
Function: Combine multiple 5C data files into a single file without needing to reload the data.
Usage: hifive 5c-combine-replicates [-h] [-q] output replicate [replicate ...]
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