Command line usage

After installation, tidesurf can be run from the command line. The following usage information is displayed when running the program with the -h or --help flag:

usage: tidesurf [-h] [-v] [--orientation {sense,antisense}] [-o OUTPUT]
            [--no_filter_cells]
            [--whitelist WHITELIST | --num_umis NUM_UMIS]
            [--min_intron_overlap MIN_INTRON_OVERLAP]
            [--multi_mapped_reads]
            SAMPLE_DIR GTF_FILE

Program: tidesurf (Tool for IDentification and Enumeration of Spliced and Unspliced Read Fragments)
Version: 0.2.1

positional arguments:
  SAMPLE_DIR            Sample directory containing Cell Ranger output.
  GTF_FILE              GTF file with transcript information.

options:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  --orientation {sense,antisense}
                        Orientation of reads with respect to transcripts. For
                        10x Genomics, use 'sense' for three prime and
                        'antisense' for five prime.
  -o OUTPUT, --output OUTPUT
                        Output directory.
  --no_filter_cells     Do not filter cells.
  --whitelist WHITELIST
                        Whitelist for cell filtering. Set to 'cellranger' to
                        use barcodes in the sample directory. Alternatively,
                        provide a path to a whitelist.
  --num_umis NUM_UMIS   Minimum number of UMIs for filtering a cell.
  --min_intron_overlap MIN_INTRON_OVERLAP
                        Minimum number of bases that a read must overlap with
                        an intron to be considered intronic.
  --multi_mapped_reads  Take reads mapping to multiple genes into account
                        (default: reads mapping to more than one gene are
                        discarded).