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YeoLab / outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
http://yeolab.github.io/outrigger/
BSD 3-Clause "New" or "Revised" License
62 stars 22 forks source link

Save events as gff files #8

Open olgabot opened 8 years ago

olgabot commented 8 years ago

Since gff files have specific parent/child structure, they are a natural fit for representing splicing events as isoforms. Additionally, the gff files created by outrigger can be combined with the original gtf/gff files for ease of biological annotation, e.g. protein translation.

The IDs in the gff files would have to be exon-based to be unique: exon1@exon2@exon3 so in events.csv, we would have to add a exon_based_event_id column, in addition to the current event_id which is junction based (e.g. for SE isoform1=junction13|isoform2=junction12@exon2@junction23)

olgabot commented 8 years ago

The idea here is to be backwards-compatible with other alternative splicing quantifiers like MISO and MAJIQ