Reference Code backup Executable files
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.
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]
plotEnrichment is a tool from the deepTools suite. The information on this page is based on deepTools version 3.5.1.
–bamfiles, -b List of indexed bam files separated by spaces.
–BED Limits the enrichment analysis to the regions specified in these BED/GTF files. Enrichment is calculated as the number of reads overlapping each feature type. The feature type is column 3 in a GTF file and “peak” for BED files.
–plotFile, -o File to save the plot to. The file extension determines the format, so heatmap.pdf will save the heatmap in PDF format. The available formats are: .png, .eps, .pdf and .svg.
–labels, -l User defined labels instead of default labels from file names. Multiple labels have to be separated by spaces, e.g. –labels sample1 sample2 sample3
–regionLabels For BED files, the label given to its region is the file name, but this can be overridden by providing a custom label. For GTF files this is ignored. Note that if you provide labels, you MUST provide one for each BED/GTF file, even though it will be ignored for GTF files.
–plotTitle, -T Title of the plot, to be printed on top of the generated image. Leave blank for no title.
–plotFileFormat Possible choices: png, pdf, svg, eps Image format type. If given, this option overrides the image format based on the plotFile ending. The available options are: png, eps, pdf and svg.
–outRawCounts Save the counts per region to a tab-delimited file.
–perSample Group the plots by sample, rather than by feature type (the default).
–variableScales By default, the y-axes are always 0-100. This allows the axis range to be restricted.
–plotHeight Plot height in cm.
–plotWidth Plot width in cm. The minimum value is 1 cm.
–colors List of colors to use for the plotted lines. Color names and html hex strings (e.g., #eeff22) are accepted. The color names should be space separated. For example, –colors red blue green
–numPlotsPerRow Number of plots per row
–alpha The alpha channel (transparency) to use for the bars. The default is 0.9 and values must be between 0 and 1.
–Offset Uses this offset inside of each read as the signal. This is useful in cases like RiboSeq or GROseq, where the signal is 12, 15 or 0 bases past the start of the read. This can be paired with the –filterRNAstrand option. Note that negative values indicate offsets from the end of each read. A value of 1 indicates the first base of the alignment (taking alignment orientation into account). Likewise, a value of -1 is the last base of the alignment. An offset of 0 is not permitted. If two values are specified, then they will be used to specify a range of positions. Note that specifying something like –Offset 5 -1 will result in the 5th through last position being used, which is equivalent to trimming 4 bases from the 5-prime end of alignments.
–version show program’s version number and exit
–region, -r Region of the genome to limit the operation to - this is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example –region chr10 or –region chr10:456700:891000.
–blackListFileName, -bl A BED or GTF file containing regions that should be excluded from all analyses. Currently this works by rejecting genomic chunks that happen to overlap an entry. Consequently, for BAM files, if a read partially overlaps a blacklisted region or a fragment spans over it, then the read/fragment might still be considered. Please note that you should adjust the effective genome size, if relevant.
–numberOfProcessors, -p Number of processors to use. Type “max/2” to use half the maximum number of processors or “max” to use all available processors.
–verbose, -v Set to see processing messages.
–keepExons For BED12 files, use each exon as a region, rather than columns 2/3
–extendReads, -e This parameter allows the extension of reads to fragment size. If set, each read is extended, without exception. NOTE: This feature is generally NOT recommended for spliced-read data, such as RNA-seq, as it would extend reads over skipped regions. Single-end: Requires a user specified value for the final fragment length. Reads that already exceed this fragment length will not be extended. Paired-end: Reads with mates are always extended to match the fragment size defined by the two read mates. Unmated reads, mate reads that map too far apart (>4x fragment length) or even map to different chromosomes are treated like single-end reads. The input of a fragment length value is optional. If no value is specified, it is estimated from the data (mean of the fragment size of all mate reads).
–ignoreDuplicates If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate’s position also has to coincide to ignore a read.
–minMappingQuality If set, only reads that have a mapping quality score of at least this are considered.
–centerReads By adding this option, reads are centered with respect to the fragment length. For paired-end data, the read is centered at the fragment length defined by the two ends of the fragment. For single-end data, the given fragment length is used. This option is useful to get a sharper signal around enriched regions.
–samFlagInclude Include reads based on the SAM flag. For example, to get only reads that are the first mate, use a flag of 64. This is useful to count properly paired reads only once, as otherwise the second mate will be also considered for the coverage.
–samFlagExclude reads based on the SAM flag. For example, to get only reads that map to the forward strand, use –samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand.
–minFragmentLength The minimum fragment length needed for read/pair inclusion. This option is primarily useful in ATACseq experiments, for filtering mono- or di-nucleosome fragments.
–maxFragmentLength The maximum fragment length needed for read/pair inclusion.