How to annotate a list of regions

[Beth Marosy]

Hello UCSC,

 

I am trying to figure out how to upload a list a defined regions, and output a corresponding gene name/symbol to go with each region and need your help.  I have tried to utilize the table browser, selecting the Gene/GenePredictions group, UCSC Genes track, and knownGene table.  Then selecting define regions and pasting a list.  Using the output format, I can select which fields I want to display in the output.  However, when I get the output it doesn’t match the gene name to the input list, I only get the gene name.  Is there a way to match the output to the input, so I know which gene goes to which defined region from the input??  Also, I have a very large list of regions that I need to do this with (207,000) – is there a way to do this with larger files?

 

Thanks for your help!!

Best,
Beth Marosy

[Steve Heitner]

Hello, Beth.

Unfortunately, there is no way to feed Table Browser input into the output.  Also, it is possible to create a custom track of your genomic coordinates and create an intersection with a gene track to overcome the 1,000-region limitation, but when doing that, it limits the output formats available and you no longer have the ability to select the fields you would like in your output.  My best suggestion in this type of situation would be to break up your query by chromosome, but with over 200K regions, this would still give you an average of ~10K regions per chromosome which is still well over the limit.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users.  If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Steve Heitner
UCSC Genome Bioinformatics Group

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