getting the correspondence between tracks and tables in hg19

[Matteo D'Antonio]

Hello, I am using Gviz in R to create some figures of ChIP-seq peaks from several different cell lines. I always need to specify track and table to access to them and I was wondering whether the UCSC website has a list of the correspondences between tracks and tables, which I might use in an automatic way.

Thank you

 

 

Dr. Matteo D'Antonio, Ph.D.

Postdoctoral Scholar, Kelly A. Frazer group

UCSD - Leichtag Family Foundation Biomedical Research Building

3500 Gilman Dr.

La Jolla, CA 92093-0761

 

[Luvina Guruvadoo]

Hello Matteo,

Thanks for your question. You can access our public MySQL server directly (http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29) and query the trackDb table for any database (hg19, for example) to obtain track names and their associated tables. Here's the schema for trackDb: http://genome.ucsc.edu/cgi-bin/hgTables?hgta_doSchemaDb=hg19&hgta_doSchemaTable=trackDb.The RMySQL package in R should allow you to connect to our MySQL databases.

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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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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