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.