Mapping reads on small reference genomes
Hi...
I need to align reads of miRNA sequencing on 2 small genomes of 2 virus. I use currently bowtie2 in --very-sensitive-local mode. There is an specific mode for this small genomes? What is the best mode of alignment for this type of mapping?
Thank you
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Your miRNA's are 21b? And your virus around ..k in x segments?
I have found bbmap to work best.