``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. |OutriggerPsi| .. |OutriggerPsi| image:: ../_static/outrigger_psi-1x.png :target: ../_static/outrigger_psi-300ppi.png 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 .. _outrigger index: outrigger_index.html .. _outrigger validate: outrigger_validate.html