pachterlab
Read GTF and get trans=> gene mapping
There is probably some way to do this in general for any annotation in BioConductor. It is easy to do using biomaRt for Ensembl, but that's insufficient.
It's probably best to keep this functionality inside R so users don't have to do more processing outside of R (e.g. adding another tool to kallisto).
@pmelsted this is probably something you can work on that doesn't require a ton of overhead. I can set up the basic Rcpp today and you can hack on it. Will tell you more over bike ride.
See TxDbLite for a way to do this directly from Ensembl FASTA files. Tested on mouse and human v80 and v81, cDNA and ncRNA. Exon mapping requires the GTF. I'll document TxDbLite a little better
