Question on gencode gene track bed file

[Sergey Yaklich]

To whom it may concern,

How could I get the gencode genes track bed file for the mouse genome mm10 from the UCSC table browser? I greatly appreciate your help.

Thank you,

Sergey Yaklichkin 

[Matthew Speir]

Hello, Sergey.

Thank you for your question about getting GENCODE information from the UCSC Genome Browser. 

You can get a BED file of all transcripts in the GENCODE VM20 track from the Table Browser using the following steps:

1. Navigate to the Table Browser, https://genome.ucsc.edu/cgi-bin/hgTables.
2. Make the following selections:
• clade: Mammal
• genome: Mouse
• assembly: Dec. 2011 (GRCm38/mm10)
• group: Genes and Gene Predictions
• track: GENCODE VM20
• table: knownGene
• region: genome
• output format: BED - browser extensible data
• output file: enter a name to save results to a file
3. Click 'Get output'.
4. Configure your output options
5. Click 'get BED'

Your output should look like:

chr12	56691766	56712707	ENSMUST00000153250.8	0	+	56695860	56709907	0	5	13,394,627,143,3055,	0,3704,4807,8245,17886,

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

Training videos & resources: http://genome.ucsc.edu/training/index.html
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Matthew Speir

Outreach, User Experience, Quality Assurance and User Support

HCA, CIRM, and UCSC Genome Browser

UCSC Genomics Institute