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Extract Y chromosome genes from the mc57bl6nj_gene_ensembl dataset? No Y filter?

Hi everyone,

I am trying to extract all Y chromosome genes from the mus musculus C57/B6 genome dataset ("mc57bl6nj_gene_ensembl") using biomaRt in R. The purpose is to create a list so I can extract Y chromosome gene counts later in my single-cell analysis pipeline.

My code worked successfully for extracting X chromosome genes (below). However, I noticed that the only values for the filter "chromosome_name" are chromosomes 1-19 and chromosome X. When I tried a value "Y" instead, I got 0 entries. 

library("biomaRt")

mc57bl6nj = useMart("ENSEMBL_MART_MOUSE",
                dataset="mc57bl6nj_gene_ensembl")
mc57bl6nj_x_genes <- getBM(attributes="external_gene_name", filters = "chromosome_name", values = "X", mart = mc57bl6nj) 
head(mc57bl6nj_x_genes)
dim(mc57bl6nj_x_genes)

Do you know why the "Y" chromosome is missing? Is there another way I can extract all Y chromosome genes?

PS, first post; apologies for any formatting issues. Also new to genome science in general.

Thanks!

From, Eva

biomart r genome sequence gene
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updated by zx8754 zx8754 • written by eknichols • eknichols

1 answer

There is no Y chromosome for that genome. Unfortunately, it's just not possible.

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written by Emily Emily

It's not unusual for highly repetitive and otherwise difficult to sequence loci, such as sex or organelle chromosomes to be skipped by smaller sequencing projects, such as the mouse strain project that produced this genome.

The link you give here is not for that genome, however, it's for the mouse reference, which is produced by the GRC and has a high quality genome. You can get those genes using BioMart, just use the mouse genes mart.

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written by Emily Emily

OH that makes sense--thanks for clarifying :) I will try that and hopefully there aren't so many differences between GRC and B6 when it comes to geneIDs on the Y chromosome!

From Eva

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written by eknichols • eknichols

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