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I am trying to do a cross-species single cell RNA sequencing integration using Seurat with a zebrafish dataset and a chick dataset. I have generated seurat objects for both. How can I use Ensemble ID (bioMart) to convert chick genes dataset to those of the zebrafish and apply this to the Seurat object for integration?

Phil
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Sam
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  • Do zebrafish and chick have a one-to-one ortholog genome? Else you will probably need to blast all your zebra genes unto the chick genome and pick the lowest E-score (or use some application that does this) for each gene. I doubt you can do it just based on EID – Baraliuh Jul 26 '22 at 16:53
  • Thank you for your reply, since I posted this I've found nearly 20,000 orthologous one2one genes between them of them using biomaRt, I'm just still having issues reassigning features. – Sam Jul 26 '22 at 21:12

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