psi: Calculate percent spliced-in (Psi/Ψ) scores for your data from the splicing events you created

Overview

outrigger psi uses the splicing events created by outrigger index, or, if outrigger validate has been run, only the valid alternative splicing events with appropriate splice sites.

Inputs

If you used the default output folders for outrigger index and outrigger validate, then you can use the command,

outrigger psi

To run the percent spliced-in calculation.

The above command is equivalent to specifying all the arguments with their default values:

outrigger psi --index ./outrigger_index --min-reads 10

Below is the full usage output when you outrigger psi -h:

$ outrigger psi -h
usage: outrigger psi [-h] [-i INDEX] [-o OUTPUT]
                     [-c COMPILED_JUNCTION_READS | -j [SJ_OUT_TAB [SJ_OUT_TAB ...]]
                     | -b [BAMS [BAMS ...]]] [-m MIN_READS]
                     [--ignore-multimapping] [--reads-col READS_COL]
                     [--sample-id-col SAMPLE_ID_COL]
                     [--junction-id-col JUNCTION_ID_COL] [--debug]
                     [--n-jobs N_JOBS]

optional arguments:
  -h, --help            show this help message and exit
  -i INDEX, --index INDEX
                        Name of the folder where you saved the output from
                        "outrigger index" (default is
                        ./outrigger_output/index, which is relative to the
                        directory where you called this program, assuming you
                        have called "outrigger psi" in the same folder as you
                        called "outrigger index")
  -o OUTPUT, --output OUTPUT
                        Name of the folder where you saved the output from
                        "outrigger index" (default is ./outrigger_output,
                        which is relative to the directory where you called
                        the program). Cannot specify both an --index and
                        --output with "psi"
  -c COMPILED_JUNCTION_READS, --compiled-junction-reads COMPILED_JUNCTION_READS
                        Name of the compiled splice junction file to calculate
                        psi scores on. Default is the '--output' folder's
                        junctions/reads.csv file. Not required if you specify
                        SJ.out.tab files with '--sj-out-tab'
  -j [SJ_OUT_TAB [SJ_OUT_TAB ...]], --sj-out-tab [SJ_OUT_TAB [SJ_OUT_TAB ...]]
                        SJ.out.tab files from STAR aligner output. Not
                        required if you specify a file with "--compiled-
                        junction-reads"
  -b [BAMS [BAMS ...]], --bams [BAMS [BAMS ...]]
                        Bam files to use to calculate psi on
  -m MIN_READS, --min-reads MIN_READS
                        Minimum number of reads per junction for calculating
                        Psi (default=10)
  --ignore-multimapping
                        Applies to STAR SJ.out.tab files only. If this flag is
                        used, then do not include reads that mapped to
                        multiple locations in the genome, not uniquely to a
                        locus, in the read count for a junction. If inputting
                        "bam" files, then this means that reads with a mapping
                        quality (MAPQ) of less than 255 are considered
                        "multimapped." This is the same thing as what the STAR
                        aligner does. By default, this is off, and all reads
                        are used.
  --reads-col READS_COL
                        Name of column in --splice-junction-csv containing
                        reads to use. (default='reads')
  --sample-id-col SAMPLE_ID_COL
                        Name of column in --splice-junction-csv containing
                        sample ids to use. (default='sample_id')
  --junction-id-col JUNCTION_ID_COL
                        Name of column in --splice-junction-csv containing the
                        ID of the junction to use. Must match exactly with the
                        junctions in the index.(default='junction_id')
  --debug               If given, print debugging logging information to
                        standard out
  --n-jobs N_JOBS       Number of threads to use when parallelizing psi
                        calculation and file reading. Default is -1, which
                        means to use as many threads as are available.

Outputs

Now the outrigger_output folder has psi subfolder, with the MXE and SE events separate.

$ tree outrigger_output
outrigger_output
├── index
│   ├── gtf
│   │   ├── gencode.vM10.annotation.subset.gtf
│   │   ├── gencode.vM10.annotation.subset.gtf.db
│   │   └── novel_exons.gtf
│   ├── junction_exon_direction_triples.csv
│   ├── mxe
│   │   ├── event.bed
│   │   ├── events.csv
│   │   ├── exon1.bed
│   │   ├── exon2.bed
│   │   ├── exon3.bed
│   │   ├── exon4.bed
│   │   ├── intron.bed
│   │   ├── splice_sites.csv
│   │   └── validated
│   │       └── events.csv
│   └── se
│       ├── event.bed
│       ├── events.csv
│       ├── exon1.bed
│       ├── exon2.bed
│       ├── exon3.bed
│       ├── intron.bed
│       ├── splice_sites.csv
│       └── validated
│           └── events.csv
├── junctions
│   ├── metadata.csv
│   └── reads.csv
└── psi
    ├── mxe
    │   └── psi.csv
    ├── outrigger_psi.csv
    └── se
        └── psi.csv

10 directories, 26 files