Question

How to convert mouse gene symbols to chicken gene symbols?

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4.5 years ago

david.f.stein ▴ 10

I have a gene-count matrices from chicken and mouse samples processed via cellranger. I am attempting to analyze them using Seurat's multi-dataset vignette. I need to convert the gene names from one of the samples to their orthologous names in the other sample. There are plenty of examples mapping from human to mouse, but I'm not sure how to do it for mouse and chicken. I was thinking I could go from mouse to human and then from human to chicken, but is there a more straightforward way?

RNA-Seq annotation genome gene R • 1.1k views

ADD COMMENT • link updated 4.5 years ago by GenoMax 148k • written 4.5 years ago by david.f.stein ▴ 10

score 2 · Accepted Answer · 2020-06-15

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4.5 years ago

GenoMax 148k

That information is already in this mapping file provided by MGI/Jackson Labs.

ADD COMMENT • link 4.5 years ago by GenoMax 148k

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Is that queryable via some API? I'm trying to convert the names in R

ADD REPLY • link 4.5 years ago by david.f.stein ▴ 10

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You can download the file and parse locally. It is not that large.

ADD REPLY • link 4.5 years ago by GenoMax 148k