Question about table brower

[Jiang, Huige]

Hi,

Could you please give me some instructions on how to get all transcription start site coordinates of all hg19 genes using your browser table?

Thank you!

Irene

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[Jairo Navarro Gonzalez]

Hello Irene,

Thank you for using the UCSC Genome Browser and your inquiry.

You can get the transcription start sites for the entire hg19 genome by first going to the Table Browser. Once there, you can configure the Table Browser setting to use the proper gene set. In my example, I will be using the UCSC Genes dataset, but you can use whichever dataset works for your research.

Step 1: Configure Table Browser Settings

Clade: Mammal 
Genome: Human
Assembly: Feb. 2009 (GRCh37/hg19) 
Group: Genes and Gene Predictions 
Track: UCSC Genes 
Region: genome
Output format: selected fields from primary and related tables

Step 2: Create a filter for each strand

Once you have set these settings, you will need to filter your Table Browser results to do two queries, one that filters for strand = '+' and uses txStart, and one that filters for strand = '-' and uses txEnd. This is because, for annotations on the negative strand, txEnd is the transcription start site. To filter for each strand, next to the filter: option, click create.

For the positive (+) strand, your filter will be: strand does match +
For the negative (-) strand, your filter will be: strand does match -

Step 3: Select output

After configuring the Table Browser settings, click get output. You will be taken to a new page where you can select the fields that interest you. For this example, I will be getting the name, chrom, strand, and txStart fields from the UCSC Genes dataset.

If you are filtering for the positive strand, choose txStart
If you are filtering for the negative strand, choose txEnd

Here is a small sample of the output I received:

#name    chrom    strand    txStart
uc001aaa.3    chr1    +    11873
uc010nxr.1    chr1    +    11873
uc010nxq.1    chr1    +    11873

Please note since we store our coordinates internally as half-open as described in our blog post, The UCSC Genome Browser Coordinate Counting Systems, you will need to add one to the txStart value for coordinates on the positive strand.

You may find this previously answered question useful for further guidance in filtering the transcription start sites for a particular gene symbol. Feel free to also search our mailing list archives for further guidance.

https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome

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.

Jairo Navarro 
UCSC Genome Browser

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