exon positions and lengths

Question

[jannetta.steyn]

Hi All

I have a bed file with the first five columns in place and I want to extend it with exon information for displaying in Galaxy. I need to add the exons lengths and start positions. I would like to extract this information from the UCSC database using command line mysql. Which tables would hold this information. There are hundreds of tables and I can't find any information on what data is in what table. Maybe I have been looking in the wrong places.

Any help would be appreciated.

Regards

Jannetta

[jannetta.steyn]

Hi Sean

I know the table browser and I have used it but it does not make a great deal of sense to me at the best of times. I'm not a GUI person. Also, I need to extract information programmatically to process a load of bed files for viewing in Galaxy.

Regards
Jannetta

[Sean Davis]

So, what is represented by your bed file? Are they genes, or something else?

[jannetta.steyn]

The file contains exons

[Sean Davis]

So, if your bed file contains exon starts and ends, what other information would you like to add to each record?

Answer 1

[Sean Davis]

A great resource for accessing UCSC genome browser information is the table browser. The table browser exposes the mysql tables in a logical way. Using the UCSC mysql tables directly can definitely be challenging.

https://genome.ucsc.edu/cgi-bin/hgTables

[jannetta.steyn]

I just discovered the "Describe table schema" button which gives me the information that I want but you still have to select loads of "things" from other dropboxes that I don't find intuitive at all.