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genome index file

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

rna-seq
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updated by Biostar Biostar • written by amy16 • amy16

1 answer

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.

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written by h.mon h.mon

I refer to hisat2-build.

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written by amy16 • amy16

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

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written by h.mon h.mon

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?

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written by amy16 • amy16

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