Reference Code backup Executable files
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.
plotFingerprint -b treatment.bam control.bam -plot fingerprint.png
plotFingerprint 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
–plotFile, -plot File name of the output figure. The file ending will be used to determine the image format. The available options are typically: “png”, “eps”, “pdf” and “svg”, e.g. : fingerprint.png.
–outRawCounts Output file name to save the read counts per bin.
–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 Exclude 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.
–labels, -l List of labels to use in the output. If not given, the file names will be used instead. Separate the labels by spaces.
–binSize, -bs Window size in base pairs to sample the genome.
–numberOfSamples, -n Number of bins that sampled from the genome, for which the overlapping number of reads is computed.
–plotFileFormat Possible choices: png, pdf, svg, eps
image format type. If given, this option overrides the image format based on the ending given via –plotFile ending. The available options are: “png”, “eps”, “pdf” and “svg”
–plotTitle, -T Title of the plot, to be printed on top of the generated image. Leave blank for no title.
–skipZeros If set, then regions with zero overlapping readsfor all given BAM files are ignored. This will result in a reduced number of read counts than that specified in –numberOfSamples
–outQualityMetrics Quality metrics can optionally be output to this file. The file will have one row per input BAM file and columns containing a number of metrics. Please see the online documentation for a longer explanation: http://deeptools.readthedocs.io/en/latest/content/feature/plotFingerprint_QC_metrics.html .
–JSDsample Reference sample against which to compute the Jensen-Shannon distance and the CHANCE statistics. If this is not specified, then these will not be calculated. If –outQualityMetrics is not specified then this will be ignored. The Jensen-Shannon implementation is based on code from Sitanshu Gakkhar at BCGSC. The CHANCE implementation is based on code from Matthias Haimel.
–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.