I am trying to use Bowtie to align RNA-seq fastq files to a set of small reference fasta files (i.e., ribosomal reference, mitochondrial reference, all for human). I've learned some groups have done that, but technically, I don't know how to implement that.
As far as I know, Bowtie does not directly align your fastq reads to the *.fasta files, you need to first build indexes using the *.fasta file(s), and then align the reads against the indexed reference. So, what I have now is a set of small reference fasta files, how can I directly align the reads against these multiple reference fasta files without indexing them first? Is that doable in bowtie?