--nvrna tag from flair align was implementing different minimap2 flags that I thought it was: "-uf" is strand specific for splicing edges, rather than the mapping. Carrying over that flag from flair align to flair quantify does not work as intended (b/c mapping to a genome is not the same as mapping to a ~transcriptome).
Going to add a --for_only (direct RNA) and --rev_only (direct cDNA) flag to flair quantify for my own usages. I'll make a pull request, but not sure if it's necessary for other folks.
Reverts BrooksLabUCSC/flair#246
--nvrna tag from flair align was implementing different minimap2 flags that I thought it was: "-uf" is strand specific for splicing edges, rather than the mapping. Carrying over that flag from flair align to flair quantify does not work as intended (b/c mapping to a genome is not the same as mapping to a ~transcriptome).
Going to add a --for_only (direct RNA) and --rev_only (direct cDNA) flag to flair quantify for my own usages. I'll make a pull request, but not sure if it's necessary for other folks.