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kallisto with reference genome

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

rna-seq kallisto
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written by vm.higareda • vm.higareda

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.

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written by h.mon h.mon

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