I need to pseudo-align my paired reads to the transcriptome using Kallisto. I know that Kallisto does not use a reference genome sequence, and instead it performs pseudo-alignment to determine the compatibility of reads with targets (e.g. transcript sequences).
However, to determine the compatibility of reads with target transcript sequences (to build a Kallisto transcriptome index), how can I choose my targeted reference transcriptome which is human and also Cassava Brown Streak Virus?
I mean, for running the below codes to create the Kallisto index from the transcriptome, should I specify which transcriptome I want to use (e.g. for human or for Cassava Brown Streak Virus)? If so, how to know what is the appropriate transcriptome that I should use for my targeted genomes?
cd kallisto index -i Potra01-mRNA.idx \ ~/share/Day01/data/reference/fasta/Potra01-mRNA.fa.gz
Thank you so much for your advise and guide. Best wishes