Getting pri-miRNA annotation

[Shelly M]

Hello,

Is there a way to get annotation of pri-miRNA? 

From the paper that was published last year in Genome Research it is said that those annotations should be available at UCSC browser, but I couldn't find it..

I would really appreciate your help,

Thanks

Shelly

[Christopher Lee]

Hi Shelly,

Thank you for your question about obtaining pri-miRNA annotations from the Genome Browser.
I am not sure as to the exact paper you are referring to, but you can download pri-miRNA
coordinates using the Table Browser.

1. Navigate to the Table Browser, http://genome.ucsc.edu/cgi-bin/hgTables.
2. Make the following selections:
     clade: Mammal
     genome: Human
     assembly: Dec. 2013 (GRCh38/hg38)
     group: Genes and Gene Predictions
     track: All GENCODE v23
     table: Basic (wgEncodeGencodeBasicV23)
     output: BED - browser extensible data
     output file: enter a file name to save your results to a file, or leave blank to display
     results in your browser

3. Next to "filter", click "create".
4. Select the wgEncodeGencodeAttrsV23 from the "Linked Tables" section
5. Click "allow filtering using fields in checked tables".
6. Type "miRNA" in the "geneType" and "transciptType" fields of the hg38.wgEncodeGencodeAttrsV23
based filters section.
         The "geneType" line should read: geneType does match miRNA
         The "transcriptType" line should read: transcriptType does match miRNA
7. Click "Submit".
8. Click "get output".
9. Choose your BED output formatting options, and click "get BED".

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any
further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address
are archived on a publicly-accessible forum. If your question includes sensitive data, you
may send it instead to genom...@soe.ucsc.edu.

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[Christopher Lee]

Hi Shelly,

I hadn't noticed before that you provided a link to the paper in question. It looks like
the authors of the paper set up a custom track to view their data in the Genome Browser,
you can find links to view their data on the human and mouse assemblies here:
http://www4.utsouthwestern.edu/mendell-lab/resources.html

Thanks,

[Shelly M]

Hi Christopher,

Thanks a lot for the help!

I have downloaded the data, just another small question- if they put the data o it is visible on the genome browser, does that mean that it is also updated in the table you instructed me to download?

Thanks again, I really appreciate the help :)

Shelly

[Christopher Lee]

Hi Shelly,

The wgEncodeGencodeBasicV23 table does not contain any data generated by
the Mendell Lab. For more information on how the data in the this table
was generated, please see the track description page:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=wgEncodeGencodeV23

Note that you can still download the data from the custom tracks through
the Table Browser. If you navigate from the lab's session link:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=mendelllab&hgS_otherUserSessionName=Manuscript%2Dhg19

to the Table Browser through the Tools menu at the top of the Genome
Browser page (after loading the session), you can use the custom tracks
as if they were native Genome Browser tracks and filter, intersect and
select fields from the custom tracks.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any
further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address
are archived on a publicly-accessible forum. If your question includes sensitive data, you
may send it instead to genom...@soe.ucsc.edu.

[Shelly M]

Thanks Christopher, this is exactly what I needed!