Question: display single dbSNP entry in UCSC genome browser
0
gravatar for chrisothal
5.8 years ago by
chrisothal0
United States
chrisothal0 wrote:

I am trying to figure out how to display a single dbSNP entry as a separate track in the UCSC Genome Browser instead of all the entries from the dbSNP 142 database. Is there a way to enter the rsID to only show the single SNP?

snp dbsnp genome • 1.8k views
ADD COMMENTlink modified 5.8 years ago by madkitty620 • written 5.8 years ago by chrisothal0
0
gravatar for madkitty
5.8 years ago by
madkitty620
Canada
madkitty620 wrote:

You can't modify 100% the way the genome is displayed in UCSC, though if you click on the left grey pane of the dbSNP you will have access to some options.

 

If what you're looking for isn't there, you can download the dbSNP on your computer and look at it by region or whatever criteria you have. They have a MySQL table format that you can just copy-paste in your mysql, then query what you're looking for. 

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by madkitty620

I have a specific SNP that I am interested in displaying. I want to use it as a reference point while overlaying other tracks so I have a tick at the location. Can I just paste the single MySQL entry as a custom track in the Genome Browser?

ADD REPLYlink modified 5.8 years ago • written 5.8 years ago by chrisothal0

I've figured out how to do this! Using the table browser, I can search for the specific dbSNP rsID and display it as a custom track in the genome browser.

ADD REPLYlink written 5.8 years ago by chrisothal0
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