Software Usage Function
multiBigwigSummary multiBigwigSummary BED-file -b file1.bw file2.bw -out results.npz --BED selection.bed Compute the average scores for each of the bigWig files in certain user selected regions (e.g. genes).
plotHeatmap 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] This tool creates a heatmap for scores associated with genomic regions. The program requires a matrix file generated by the tool computeMatrix
plotCorrelation plotCorrelation [-h] --corData FILE --corMethod {spearman,pearson} --whatToPlot {heatmap,scatterplot} [--plotFile FILE] [--skipZeros] [--labels sample1 sample2 [sample1 sample2 ...]] [--plotTitle PLOTTITLE] [--plotFileFormat FILETYPE] [--removeOutliers] [--version] [--outFileCorMatrix FILE] [--plotHeight PLOTHEIGHT] [--plotWidth PLOTWIDTH] [--zMin ZMIN] [--zMax ZMAX] [--colorMap] [--plotNumbers] [--xRange XRANGE XRANGE] [--yRange YRANGE YRANGE] [--log1p] This tools takes the default output of multiBamSummary or multiBigwigSummary, and computes the pairwise correlation among samples. Results can be visualized as scatterplots or as a heatmap of correlation coefficients
plotProfile 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] 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.
plotEnrichment 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] 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.
plotCoverage 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] 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.
HiFive hifive 5c-normalize <SUBCOMMAND> [-h] [-m MINDIST] [-x MAXDIST] [-r REGIONS] [-o OUTPUT] [-q] [normalization options] project Find correction parameter values using one of the available algorithms.
HiFive 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 Using an already created 5C project, generate a tabular genomic-interval file for a specified region and optional image.
HiFive 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 Using an already created 5C project, generate an HDF5-formatted heatmap file and optional image.
HiFive hifive 5c-combine-replicates [-h] [-q] output replicate [replicate ...] Combine multiple 5C data files into a single file without needing to reload the data.
HiFive hifive 5c-data [-h] (-B BAM BAM | -C COUNT) [-q] fragment output Create a data file from mapped BAM or fragment-pair counts files.
HiFive 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] Perform all of the steps of the subcommands fends, hic-data, hic-project, and hic-normalization in one command.
HiFive hifive 5c-project [-h] [-f MININT] [-m MINDIST] [-x MAXDIST] [-q] data output Create a project file, filter fragments, and estimate distance-dependence.
HiFive 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 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.
plotFingerprint plotFingerprint -b treatment.bam control.bam -plot fingerprint.png 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.
computeGCBias computeGCBias -b file.bam --effectiveGenomeSize 2150570000 -g mm9.2bit -l 200 --GCbiasFrequenciesFile freq.txt [options] 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.
HiFive hifive hic-project [-h] [-f MININT] [-m MINDIST] [-x MAXDIST] [-j MINBIN] [-n NUMBINS] [-q] data output Create a project file, filter fends, and estimate distance-dependence.
HiFive 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 Create a multi-resolution heatmap file from a HiFive HiC project file.
computeMatrix computeMatrix scale-regions -S <biwig file> -R <bed file> -b 1000 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 hic-data [-h] (-S BAM BAM | -R RAW | -M MAT | -X MATRIX) [-i INSERT] [--skip-duplicate-filtering] [-q] fend output Create a data file from mapped BAM, MAT, or paired coordinate text (RAW) files or from binned matrix files.