141 lines (136 with data), 8.9 kB

usage: htseq-count [-h] [--version] [-f {sam,bam,auto}] [-r {pos,name}]
                   [--max-reads-in-buffer MAX_BUFFER_SIZE]
                   [-s {yes,no,reverse}] [-a MINAQUAL] [-t FEATURE_TYPE]
                   [-i IDATTR] [--additional-attr ADDITIONAL_ATTRIBUTES]
                   [--add-chromosome-info]
                   [-m {union,intersection-strict,intersection-nonempty}]
                   [--nonunique {none,all,fraction,random}]
                   [--secondary-alignments {score,ignore}]
                   [--supplementary-alignments {score,ignore}] [-o SAMOUTS]
                   [-p {SAM,BAM,sam,bam}] [-d OUTPUT_DELIMITER]
                   [-c OUTPUT_FILENAME] [--counts-output-sparse]
                   [--append-output] [-n NPROCESSES]
                   [--feature-query FEATURE_QUERY] [-q] [--with-header]
                   samfilenames [samfilenames ...] featuresfilename

This script takes one or more alignment files in SAM/BAM format and a feature
file in GFF format and calculates for each feature the number of reads mapping
to it. See http://htseq.readthedocs.io/en/master/count.html for details.

positional arguments:
  samfilenames          Path to the SAM/BAM files containing the mapped reads.
                        If '-' is selected, read from standard input
  featuresfilename      Path to the GTF file containing the features

optional arguments:
  -h, --help            show this help message and exit
  --version             Show software version and exit
  -f {sam,bam,auto}, --format {sam,bam,auto}
                        Type of <alignment_file> data. DEPRECATED: file format
                        is detected automatically. This option is ignored.
  -r {pos,name}, --order {pos,name}
                        'pos' or 'name'. Sorting order of <alignment_file>
                        (default: name). Paired-end sequencing data must be
                        sorted either by position or by read name, and the
                        sorting order must be specified. Ignored for single-
                        end data.
  --max-reads-in-buffer MAX_BUFFER_SIZE
                        When <alignment_file> is paired end sorted by
                        position, allow only so many reads to stay in memory
                        until the mates are found (raising this number will
                        use more memory). Has no effect for single end or
                        paired end sorted by name
  -s {yes,no,reverse}, --stranded {yes,no,reverse}
                        Whether the data is from a strand-specific assay.
                        Specify 'yes', 'no', or 'reverse' (default: yes).
                        'reverse' means 'yes' with reversed strand
                        interpretation
  -a MINAQUAL, --minaqual MINAQUAL
                        Skip all reads with MAPQ alignment quality lower than
                        the given minimum value (default: 10). MAPQ is the 5th
                        column of a SAM/BAM file and its usage depends on the
                        software used to map the reads.
  -t FEATURE_TYPE, --type FEATURE_TYPE
                        Feature type (3rd column in GTF file) to be used, all
                        features of other type are ignored (default, suitable
                        for Ensembl GTF files: exon)
  -i IDATTR, --idattr IDATTR
                        GTF attribute to be used as feature ID (default,
                        suitable for Ensembl GTF files: gene_id). All feature
                        of the right type (see -t option) within the same GTF
                        attribute will be added together. The typical way of
                        using this option is to count all exonic reads from
                        each gene and add the exons but other uses are
                        possible as well. You can call this option multiple
                        times: in that case, the combination of all attributes
                        separated by colons (:) will be used as a unique
                        identifier, e.g. for exons you might use -i gene_id -i
                        exon_number.
  --additional-attr ADDITIONAL_ATTRIBUTES
                        Additional feature attributes (default: none, suitable
                        for Ensembl GTF files: gene_name). Use multiple times
                        for more than one additional attribute. These
                        attributes are only used as annotations in the output,
                        while the determination of how the counts are added
                        together is done based on option -i.
  --add-chromosome-info
                        Store information about the chromosome of each feature
                        as an additional attribute (e.g. colunm in the TSV
                        output file).
  -m {union,intersection-strict,intersection-nonempty}, --mode {union,intersection-strict,intersection-nonempty}
                        Mode to handle reads overlapping more than one feature
                        (choices: union, intersection-strict, intersection-
                        nonempty; default: union)
  --nonunique {none,all,fraction,random}
                        Whether and how to score reads that are not uniquely
                        aligned or ambiguously assigned to features (choices:
                        none, all, fraction, random; default: none)
  --secondary-alignments {score,ignore}
                        Whether to score secondary alignments (0x100 flag)
  --supplementary-alignments {score,ignore}
                        Whether to score supplementary alignments (0x800 flag)
  -o SAMOUTS, --samout SAMOUTS
                        Write out all SAM alignment records into SAM/BAM files
                        (one per input file needed), annotating each line with
                        its feature assignment (as an optional field with tag
                        'XF'). See the -p option to use BAM instead of SAM.
  -p {SAM,BAM,sam,bam}, --samout-format {SAM,BAM,sam,bam}
                        Format to use with the --samout option.
  -d OUTPUT_DELIMITER, --delimiter OUTPUT_DELIMITER
                        Column delimiter in output (default: TAB).
  -c OUTPUT_FILENAME, --counts_output OUTPUT_FILENAME
                        Filename to output the counts to instead of stdout.
  --counts-output-sparse
                        Store the counts as a sparse matrix (mtx, h5ad, loom).
  --append-output       Append counts output to an existing file instead of
                        creating a new one. This option is useful if you have
                        already creates a TSV/CSV/similar file with a header
                        for your samples (with additional columns for the
                        feature name and any additionl attributes) and want to
                        fill in the rest of the file.
  -n NPROCESSES, --nprocesses NPROCESSES
                        Number of parallel CPU processes to use (default: 1).
                        This option is useful to process several input files
                        at once. Each file will use only 1 CPU. It is
                        possible, of course, to split a very large input
                        SAM/BAM files into smaller chunks upstream to make use
                        of this option.
  --feature-query FEATURE_QUERY
                        Restrict to features descibed in this expression.
                        Currently supports a single kind of expression:
                        attribute == "one attr" to restrict the GFF to a
                        single gene or transcript, e.g. --feature-query
                        'gene_name == "ACTB"' - notice the single quotes
                        around the argument of this option and the double
                        quotes around the gene name. Broader queries might
                        become available in the future.
  -q, --quiet           Suppress progress report
  --with-header         Whether to add a column header to the output TSV file
                        indicating which column corresponds to which input BAM
                        file. Only used if output to console or tsv or csv
                        file. Default to False.

Written by Simon Anders (sanders@fs.tum.de), European Molecular Biology
Laboratory (EMBL), Givanna Putri (g.putri@unsw.edu.au) and Fabio Zanini
(fabio.zanini@unsw.edu.au), UNSW Sydney. (c) 2010-2021. Released under the
terms of the GNU General Public License v3. Please cite the following paper if
you use this script: G. Putri et al. Analysing high-throughput sequencing data
in Python with HTSeq 2.0. Bioinformatics (2022).
https://doi.org/10.1093/bioinformatics/btac166. Part of the 'HTSeq' framework,
version 2.0.1.