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Using UCSC mm10 for organoids

Hello,

I am trying to use GSNAP to align my reads (here are the raw reads: https://www.ncbi.nlm.nih.gov/sra?term=DRP004053), and I need a reference genome. The paper of this study used UCSC mm10, but not sure what part of it I need because the sequences I am using are just of organoids, and where do I search for this.

I appreciate your help!

assembly alignment next-gen rna-seq
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written by Moneeb Bajwa • Moneeb Bajwa

I am using are just of organoids

Forgive my ignorance about organoids, but aren't those just based on some organism and therefore share the same genome?

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written by WouterDeCoster WouterDeCoster

1 answer

As Wouter mentioned in his comment, organoids are derived from an organism and therefore have that organism's genome. So a mouse-derived organoid is mouse tissue and should be aligned against the mouse genome.

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written by Devon Ryan Devon Ryan

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