I'm using Salmon to analyze RNAseq datasets in our lab.
The cells that we perform RNAseq on were delivered with a custom gene. The sequence of the gene is codon-optimized so that it is distinct from the one in the genome. We'd like to perform transcript quantification for the codon-optimized gene.
For other tools (i.e. STAR, CellRanger), there are documentations specifying how to supply custom gene sequence during the indexing step. However for Salmon, I have not found the description for such steps in the documentation.
Does Salmon support this feature? If yes, should I simply add my sequence to the "gentrome.fa.gz" as in this tutorial?