I would like to generate a new reference for kallisto where I add GFP. I found this link: https://github.com/igordot/genomics/blob/master/workflows/ref-genome-gfp.md and it seems pretty straightforward to add the GFP for the alignment.
However, I am not sure how to proceed with assigning gene IDs. Normally, I use tximport and biomart to get the ensembl version I am using to assign gene IDs. However, that would not have the GFP. Is it ok to still do that and then at the end of my table with the counts just take the values from the raw kallisto output for GFP and add them there? Would the fact that the kallisto output has GFP but the ensembl object doesn't cause any issues with the gene name assignment?