How to get rRNA for mm39?

[Banerjee, Payal (NIH/NHGRI) [C]]

Hello,

 

I was trying to get rRNA genes for the mm39 Mouse reference genome from Table Browser. I am unable to find anything related to rRNA specifically. Can anyone please point to me how to get a rRNA bed file for mm39 from Table Browser?

 

Thanks,

Payal

[Luis Nassar]

Hello, Payal.

Thank you for your interest in the Genome Browser.

You can get the rRNA genes on mm39 using the filter option available. Due to some data issues we are currently fixing, we recommend you use our preview server with the latest VM30 GENCODE annotations.

You may access the Table Browser on our preview server here: http://genome-preview.cse.ucsc.edu/cgi-bin/hgTables

If you make the following selections:

Then select the filter button and have transcriptType match rRNA:

Those selections should result in 354 rRNA gene matches in the output file.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

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