[ ] createIndices: drop 'gtf to files', use gtfToGenePred instead? (would be consistent with repoTrampoline)
[ ] take transcript2gene.txt as input to Salmon_Alevin ("genes_t2g")
[ ] drop gene symbol annotation from velo_to_sce ? (scRNAseq_splitAlevinVelocityMatrices.R) - would relieve the requirement from gene ID to gene symbol mapping
[ ] keep filterGTF and all downstream functions only for counting, not for mapping steps (or disable completely?)
[ ] create salmon indices and update organism yamls
gtfToGenePred
instead? (would be consistent with repoTrampoline)velo_to_sce
? (scRNAseq_splitAlevinVelocityMatrices.R) - would relieve the requirement from gene ID to gene symbol mappingfilterGTF
and all downstream functions only for counting, not for mapping steps (or disable completely?)