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] [--bam_path BAM_PATH [BAM_PATH ...]]
            [--whitelist WHITELIST [WHITELIST ...] | --num_umis NUM_UMIS]
            [--min_intron_overlap MIN_INTRON_OVERLAP]
            [--multi_mapped_reads] [--export_umi_tables]
            SAMPLE_DIR GTF_FILE

Program: tidesurf (Tool for IDentification and Enumeration of Spliced and Unspliced Read Fragments)
Version: 0.4.0

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.
  --bam_path BAM_PATH [BAM_PATH ...]
                        Explicit path to one or more BAM files. The sample
                        directory will be ignored if this is given. If this
                        argument is used, the positional arguments must be
                        separated from it by another argument, by ' -- ', or
                        they must precede it.
  --whitelist WHITELIST [WHITELIST ...]
                        Whitelist for cell filtering. Set to 'cellranger' to
                        use barcodes in the sample directory. Alternatively,
                        provide a path to a whitelist. If multiple BAM files
                        are passed to 'bam_path', one whitelist can be passed
                        per BAM file. If this argument is used, the positional
                        arguments must be separated from it by another
                        argument, by ' -- ', or they must precede it.
  --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).
  --export_umi_tables   Export tables with splice type for UMIs.