I am working on the RNA-Seq project on non-model organism. The genome is not available for this organism but the mitochondria has been sequenced and published.
I want to remove all mt sequence from my original fastq files so I am going to align my reads (100bp pair-end) to mt genome. I want to use Bowtie 2. But I found Bowtie 2 is designed for "quickly aligning large sets of short DNA sequences (reads) to large genomes".
The animal mt genome is relatively small so I am wondering if Bowtie 2 still work? I want to use this because one of its output option is unmapped reads, which is exactly what I want.