rRNA from mm10

[Eleonora Adami]

Dear Bioinformatic Group,

I saw in one discussion on the google group that you suggest to retrieve rRNA info from the wgEncodeGencodeBasicV17 table, as far as the human annotation goes. What is your advice if i want to extract info for mouse mm10?

Best,

Ele

[Steve Heitner]

Hello, Ele.

I assume you are referring to the previously-answered mailing list question at https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/p-7101I71ak/G5fidhNWLlIJ.  The GENCODE and Ensembl data sets are essentially the same and fortunately, mm10 does have an Ensembl Genes track.  Perform the following steps to obtain rRNA info from the Ensembl Genes track for mm10:

1. Navigate to http://genome.ucsc.edu/cgi-bin/hgTables

2. Select the following options:
Clade: Mammal
Genome: Mouse
Assembly: Dec. 2011 (GRCm38/mm10)
Group: Genes and Gene Prediction Tracks
Track: Ensembl Genes
Table: ensGene
Region: genome

3. On the “filter” line, click the “create” button

4. In the “Linked Tables” section, check the mm10.ensemblSource checkbox

5. Click the “allow filtering using fields in checked tables” button

6. In the “mm10.ensemblSource based filters” section, the “source” line should read: source does match rRNA

7. Click the “submit” button

8. Click the “get output” button

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  All messages sent to that address are archived on a publicly-accessible Google Groups forum.  If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Steve Heitner
UCSC Genome Bioinformatics Group

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