Question

Using UCSC mm10 for organoids

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6.4 years ago

Moneeb Bajwa ▴ 10

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 • 1.1k views

ADD COMMENT • link 6.4 years ago by Moneeb Bajwa ▴ 10

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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?

ADD REPLY • link 6.4 years ago by WouterDeCoster 47k

score 3 · Accepted Answer · 2018-07-20

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6.4 years ago

Devon Ryan 104k

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.