table browser, linking bioType information to GENCODE v24

[Anton Kratz]

Dear UCSC team,

in the table browser, hg38 assembly, group: Genes and Gene Predictions, track: GENCODE v24, table: knownGene.

I am trying to link this table to information about the bioType (coding_mRNA, lncRNA_antisense, lncRNA_divergent and so on) of the Gencode genes.

Is this possible? Could you let me know which tables I need to link?

Anton

[Matthew Speir]

Hi Anton,

Thank you for your question about obtaining biotype information for transcripts in the GENCODE v24 track from the UCSC Genome Browser.

You can obtain this information from the "knownAttrs" table, specifically the "geneType" and "transcriptType" columns. In the Table Browser, you can get this information 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: Human
    assembly: Dec. 2013 (GRCh38/hg38)
    group: Genes and Gene Predictions
    track: GENCODE v24
    table: knownGene
    region: genome, a single position, or a set of regions in BED format
    output format: selected fields from primary and related tables
    output file: enter a file name or leave blank to view results in the browser

3. Click "get output".
4. Under the "Linked Tables" section, check the box next to "knownAttrs".
5. Click "allow selections from checked tables".
6. Under the "hg38.knownAttrs fields" section, check the boxes next to "geneType" and "transcriptType".
7. Check the boxes next to other fields of interest, such as "geneId" or "transcriptName".
8. Click "get output".

Detailed information about the geneType and TranscriptType values can be found on the GENCODE website here: https://www.gencodegenes.org/data_format.html, specifically under the "B.1. Mandatory fields" section.

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

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