Select local alignment or end-to-end alignment for Bowtie2 to filter rRNA
Hello, I have been working on the metatranscriptomics (2x150 bp), and I want to use Bowtie2 to align the adapter-free and high-quality sequences to the Silva rRNA database, to remove the mapped rRNA reads.
Because the reference sequences is longer than those in metatranscriptomics, I think the local alignment should be better.
Could you please give me some advices?
Thanks in advance!
Mort
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