
count_tab - Count reads per gene from flatfile using UMIs

Usage: umi_tools count_tab [OPTIONS] [--stdin=IN_TSV[.gz]] [--stdout=OUT_TSV[.gz]]

       note: If --stdin/--stdout are ommited standard in and standard
             out are used for input and output. Input/Output will be
             (de)compressed if a filename provided to --stdin/--stdout
             ends in .gz 

For full UMI-tools documentation, see https://umi-tools.readthedocs.io/en/latest/

Options:
  --version             show program's version number and exit

  count_tab-specific options:
    --barcode-separator=BC_SEP
                        separator between read id and UMI  and (optionally)
                        the cell barcode
    --per-cell          Readname includes cell barcode as well as UMI in
                        format: read[sep]UMI[sep]CB

  UMI grouping options:
    --method=METHOD     method to use for umi grouping [default=directional]
    --edit-distance-threshold=THRESHOLD
                        Edit distance theshold at which to join two UMIs when
                        grouping UMIs. [default=1]
    --spliced-is-unique
                        Treat a spliced read as different to an unspliced one
                        [default=False]
    --soft-clip-threshold=SOFT_CLIP_THRESHOLD
                        number of bases clipped from 5' end before read is
                        counted as spliced [default=4]
    --read-length       use read length in addition to position and UMI to
                        identify possible duplicates [default=False]

  Input/Output format options:
    --in-format=IN_FORMAT
                        File format of the input file. Format is usually
                        implied from the extension of the filename, but maybe
                        overridden with this option. Default=bam
    --input-options=INPUT_OPTIONS
                        Format string provided to htslib for reading. Mostly
                        useful for CRAM formatted files. See samtools
                        documentation
    -i, --in-sam        [Deprecated] Input file is in sam format
                        [default=False]
    --reference-filename=REFERENCE_FILENAME
                        File path or URL to the genome reference to be used
                        when reading or writing CRAM files. By default, when
                        reading a CRAM file, the reference recorded in the
                        input file will be used unless this is specified. When
                        writing, specifying a reference location is required.

  Input/Output pipe options:
    -I FILE, --stdin=FILE
                        file to read stdin from [default = stdin].
    -L FILE, --log=FILE
                        file with logging information [default = stdout].
    -E FILE, --error=FILE
                        file with error information [default = stderr].
    -S FILE, --stdout=FILE
                        file where output is to go [default = stdout].
    --temp-dir=FILE     Directory for temporary files. If not set, the bash
                        environmental variable TMPDIR is used[default = None].
    --log2stderr        send logging information to stderr [default = False].
    --compresslevel=COMPRESSLEVEL
                        Level of Gzip compression to use. Default (6)
                        matchesGNU gzip rather than python gzip default (which
                        is 9)

  profiling options:
    --timeit=TIMEIT_FILE
                        store timeing information in file [none].
    --timeit-name=TIMEIT_NAME
                        name in timing file for this class of jobs [all].
    --timeit-header     add header for timing information [none].

  common options:
    -v LOGLEVEL, --verbose=LOGLEVEL
                        loglevel [1]. The higher, the more output.
    -h, --help          output short help (command line options only).
    --help-extended     Output full documentation
    --random-seed=RANDOM_SEED
                        random seed to initialize number generator with
                        [none].
