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smith-chem-wisc / Spritz

Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
https://smith-chem-wisc.github.io/Spritz/
MIT License
7 stars 11 forks source link

Use snpEff.config to guide which genomes we download #118

Closed acesnik closed 4 years ago

acesnik commented 5 years ago

Take in the snpEff.config information regarding genomes and gene sets as a dictionary (e.g. key: GRCh38.81, value: tuple with genome fasta URL and GTF gene set URL)

acesnik commented 5 years ago

We can also just hard code in the URLs for non-model organisms as users need them, too. That's much easier.

acesnik commented 5 years ago

This is important for collaboration with Olivier with non-human primates. The impact of the work is much higher if we can look for variants in any organism.

acesnik commented 4 years ago

Solved with @bintiibrahim's contribution of the various Ensembl genomes