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nsalomonis / altanalyze

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.
http://www.altanalyze.org
Apache License 2.0
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A custom database #38

Closed OlgaVT closed 4 years ago

OlgaVT commented 4 years ago

Good afternoon, I did not find it in the manual but is it now possible to make an AltAnalyze compatible species database using my own annotation (for example, a custom gtf file)? Thank you!

nsalomonis commented 4 years ago

Great question! Unfortunately, there is currently no gtf to gene/transcript database converter. This was a project several years ago, but never completed as the AltAnalyze database ultimately had too many data types to reasonably create the necessary exports. All required files are be imported from the Ensembl SQL database. These include transcript, protein, protein domain and sequence information needed to build the database. Nonetheless, with available information this would be possible but still very challenging.

OlgaVT commented 4 years ago

Thank you!