validate: Check that the found exons are real

Overview

Inputs

After you run outrigger index, you have the following directory structure:

$ tree outrigger_output/index
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
│   └── se
│       ├── event.bed
│       ├── events.csv
│       ├── exon1.bed
│       ├── exon2.bed
│       ├── exon3.bed
│       └── intron.bed
└── junctions
    ├── metadata.csv
    └── reads.csv

5 directories, 19 files

The outrigger validate command relies on this structure and

This example command assumes that you have a mm10 genome fasta file located at ~/genomes/mm10/gencode/m10/GRCm38.primary_assembly.genome.fa and a chromosome sizes file located at ~/genomes/mm10/mm10.chrom.sizes

outrigger validate -f ~/genomes/mm10/gencode/m10/GRCm38.primary_assembly.genome.fa -g ~/genomes/mm10/mm10.chrom.sizes

Outputs

Now there is a new folder in the outrigger_output/index/mxe and outrigger_output/index/se folders called validated. Plus, there is a file

$ tree outrigger_output/index
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

5 directories, 21 files