kallisto with reference genome

Question

[vm.higareda]

Is it correct to use a reference genome to build a kallisto index and use this index to run kallisto quant?.

I have genome of a bacteria, extracted the complete sequence of the genes and used this multi fasta file to build the index

[h.mon]

I have genome of a bacteria, extracted the complete sequence of the genes and used this multi fasta file to build the index

What you did is correct, but it is not a "reference genome", you may call it reference gene set or simply reference transcriptome.