Mapping reads on small reference genomes

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8.6 years ago

silas008 ▴ 160

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

miRNA alignment • 1.9k views

ADD COMMENT • link updated 19 months ago by Ram 43k • written 8.6 years ago by silas008 ▴ 160

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Your miRNA's are 21b? And your virus around ..k in x segments?

ADD REPLY • link updated 19 months ago by Ram 43k • written 8.6 years ago by ALchEmiXt ★ 1.9k

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I have found bbmap to work best.

ADD REPLY • link updated 19 months ago by Ram 43k • written 8.6 years ago by Adrian Pelin ★ 2.6k

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