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?

Thanks! Ray

Yes, you would add the sequence to the reference transcriptome that is used for the gentrome construction. Simply make a separate fasta file with it and then cat the transcriptome fasta and the extra fasta file together, then use that newly created file to make your gentrome and run the indexing. By the way, salmon is not an R or Bioconductor package, for general bioinformatics question you may consider biostars.org simply because the traffic there is much higher and this forum here is intended for technical help with the Bioc package. Hope that helps.