Software usage

switchseq

Name:
    SwitchSeq - A tool for the identification, annotation and visualisation of
    extreme changes in splicing in RNA-seq experiments

Version:
    switchseq 1.0

Usage:
    switchseq [options]

Options:
    --help | -h
            Print the documentation.

    ** REQUIRED **
    --tool | -t <get_data|get_switch>
            Tool to be executed. More information about a specific tool can
            be obtained in its help page:

            switchseq -t get_data -h

switchseq -t get_data

Usage:
    switchseq -t get_data [options]

Options:
    --help | -h
            Print the documentation.

    ** REQUIRED **
    --species | -s <string>
            Species (three letter code).

    --ensembl_v | -e <integer>
            Ensembl version.

    ** OPTIONAL **
    --data_dir | -d <dir>
            Temporary data directory. [default: ./data]

switchseq -t get_switch

Usage:
    switchseq -t get_switch [options]

Options:
    --help | -h
            Print the documentation.

    ** REQUIRED **
    --input | -i <file>
            Input file. Columns have to be specified as follows: gene_id (1)
            transcript_id (2) transcript expression levels in each sample (3-). Eg, for
            an experiment with 3 controls and 3 KO, column names could be
            the following:

            gene_id transcript_id C1 C2 C3 KO1 KO2 KO3

            Fields can be delimited by any number of spaces or tabs.
            Technical replicates are supported. Those are automatically
            detected by SwitchSeq whenever non-unique column names are used.

    --cond1 | -c1 <interval>
            Columns for condition 1. [example: --cond1 3-5]

    --cond2 | -c2 <interval>
            Columns for condition 2. [example: --cond2 6-8]

    --species | -s <string>
            Species (three letter code).

    --ensembl_v | -e <integer>
            Ensembl version.

    ** OPTIONAL **
    --out_dir | -o <dir>
            html output directory. [default: ./html]

    --data_dir | -d <dir>
            Data directory containing information from Ensembl and APPRIS.
            [default: ./data]

    --threshold_gexp | -g <float>
            Gene expression threshold. [default: 0.01]

    --threshold_breadth | -b <float>
            Expression breadth threshold. [default: 50]

    --threshold_dominance | -dom <float>
            Dominance threshold. [default: 1]

    --filt | -f <file>
            List of transcript ids that undergo differential usage across
            the studied conditions. [default: NA]

            The file must be in the following format, with no headers:

            gene_id transcript_id