Photinus pyralis Official Geneset

This is the Official Geneset (OGS) for Photinus pyralis (Big Dipper Firefly)

As reported in this preprint: https://www.biorxiv.org/content/early/2018/02/25/237586

Genome version: Ppyr1.3
Geneset version: PPYR_OGS1.0

This GIT repository is meant to keep track of any changes to the OGS, and hopefully have a useful audit log which describes what changes occured.

Also see: fireflybase.org

Where can I download an official version of the data?

See Releases

Dependencies

(Executable from your local command line)

• gt
• igvtools (also available in IGV GUI)
• seqkit
• gffutils

Reporting gene model problems

Report issues here

Making direct gene model or annotation changes

1. Fork this repository
2. Download and edit the PPYR_OGS*.gff3 file
3. Sort the GFF3 file and regenerate dependent files (CDS, mRNA, peptide) files using the utility_scripts/sort-and-regenerate-OGS-GFF.sh script.
4. Commit your changes back to your repository, with an informative message for the changes that were made
5. Submit a pull request to this repository
6. If all looks good I'll merge the pull request

Future

Get a proper relational database ala Chado, and/or a collaborative GUI editing interface, ala Apollo.

License

Data files (e.g. geneset .fa.gz files, gff3 files) are licensed under the Creative Commons CC-BY-SA 4.0 International license. Software (e.g. BASH scripts) is licensed under the MIT license