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. Currently this works by rejecting genomic chunks that happen to overlap an entry. The format is chr:start:end, for example –region chr10 or –region chr10:456700:891000.Ī BED or GTF file containing regions that should be excluded from all analyses. Region of the genome to limit the operation to - this is useful when testing parameters to reduce the computing time.
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The CHANCE implementation is based on code from Matthias Haimel. The Jensen-Shannon implementation is based on code from Sitanshu Gakkhar at BCGSC. If –outQualityMetrics is not specified then this will be ignored. If this is not specified, then these will not be calculated. Reference sample against which to compute the Jensen-Shannon distance and the CHANCE statistics. Please see the online documentation for a longer explanation. The file will have one row per input BAM file and columns containing a number of metrics. Quality metrics can optionally be output to this file. This will result in a reduced number of read counts than that specified in –numberOfSamples If set, then regions with zero overlapping readsfor all given BAM files are ignored. Title of the plot, to be printed on top of the generated image. The available options are: “png”, “eps”, “pdf”, “plotly” and “svg” If given, this option overrides the image format based on the ending given via –plotFile ending. Possible choices: png, pdf, svg, eps, plotly The number of bins that are sampled from the genome, for which the overlapping number of reads is computed. This times –numberOfSamples should be less than the genome size. Window size in base pairs to sample the genome. Instead of manually specifying labels for the input BAM/bigWig files, this causes deepTools to use the file name after removing the path and extension. If not given, the file names will be used instead. The maximum fragment length needed for read/pair inclusion. This option is primarily useful in ATACseq experiments, for filtering mono- or di-nucleosome fragments. The minimum fragment length needed for read/pair inclusion. 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. (Default: None)Įxclude reads based on the SAM flag. This is useful to count properly paired reads only once, as otherwise the second mate will be also considered for the coverage. For example, to get only reads that are the first mate, use a flag of 64.
This option is useful to get a sharper signal around enriched regions. For single-end data, the given fragment length is used. For paired-end data, the read is centered at the fragment length defined by the two ends of the fragment. If set, only reads that have a mapping quality score of at least this are considered.īy adding this option, reads are centered with respect to the fragment length. If reads are paired, the mate’s position also has to coincide to ignore a read. If set, reads that have the same orientation and start position will be considered only once. If no value is specified, it is estimated from the data (mean of the fragment size of all mate reads). The input of a fragment length value is optional. Unmated reads, mate reads that map too far apart (>4x fragment length) or even map to different chromosomes are treated like single-end reads. Paired-end: Reads with mates are always extended to match the fragment size defined by the two read mates. Reads that already exceed this fragment length will not be extended. Single-end: Requires a user specified value for the final fragment length. NOTE: This feature is generally NOT recommended for spliced-read data, such as RNA-seq, as it would extend reads over skipped regions. If set, each read is extended, without exception. This parameter allows the extension of reads to fragment size. Read processing options ¶ -extendReads, -e