microRNA annotation

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shamsher jagat

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Apr 28, 2016, 10:10:25 AM4/28/16

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How can I download microRNA annotation (bed/ GTF) for GRCH37 or hg19

Thanks

Kanwar

Matthew Speir

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Apr 28, 2016, 2:05:35 PM4/28/16

to shamsher jagat, gen...@soe.ucsc.edu

Hi Kanwar,

Thank you for your question about obtaining miRNA annotations for hg19
from the UCSC Genome Browser.

You can obtain a BED file of miRNAs from the Table Browser using the
following steps:

1. Navigate to the Table Browser, http://genome.ucsc.edu/cgi-bin/hgTables.
2. Make the following selections:
clade: Mammal
genome: Human
assembly: Feb. 2009 (GRCh37/hg19)
group: Genes and Gene Predictions
track: GENCODE Genes V19
table: Basic (wgEncodeGencodeBasicV19)
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 wgEncodeGencodeAttrsV19 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
hg19.wgEncodeGencodeAttrsV19 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".

I hope this is helpful. 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 Google Groups forum. If your question includes
sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group