Question: exon positions and lengths
0
gravatar for jannetta.steyn
5.0 years ago by
United Kingdom
jannetta.steyn0 wrote:

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

exons • 978 views
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by jannetta.steyn0

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

ADD REPLYlink modified 12 months ago by _r_am31k • written 5.0 years ago by jannetta.steyn0

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

ADD REPLYlink modified 12 months ago by _r_am31k • written 5.0 years ago by Sean Davis26k

The file contains exons

ADD REPLYlink written 5.0 years ago by jannetta.steyn0

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

ADD REPLYlink modified 12 months ago by _r_am31k • written 5.0 years ago by Sean Davis26k
0
gravatar for Sean Davis
5.0 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

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

ADD COMMENTlink modified 12 months ago by _r_am31k • written 5.0 years ago by Sean Davis26k

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.

ADD REPLYlink modified 12 months ago by _r_am31k • written 5.0 years ago by jannetta.steyn0
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