Question

genome index file

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7.1 years ago

amy16 ▴ 40

Can u please advise me if I should go for large or small genome index for Cicer genome size of 740 Mbp?

RNA-Seq • 2.7k views

ADD COMMENT • link updated 5.8 years ago by Biostar 20 • written 7.1 years ago by amy16 ▴ 40

score 0 · Answer 1 · 2017-11-06

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7.1 years ago

h.mon 35k

Are you talking about bowtie2? The manual says the appropriate index will be selected automatically. Are you talking about something else? Read How To Ask Good Questions On Technical And Scientific Forums and edit your question after that.

ADD COMMENT • link 7.1 years ago by h.mon 35k

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I refer to hisat2-build.

ADD REPLY • link 7.1 years ago by amy16 ▴ 40

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So read its manual, the answer is there. In particular, read the Wrapper and Small and large indexes sections.

ADD REPLY • link 7.1 years ago by h.mon 35k

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Yeah, the manual says so, but I came across a paper where they had generated large genome index for a ref genome of size 740 Mbp. I was trying to understand why they had done so?

ADD REPLY • link 7.1 years ago by amy16 ▴ 40