query: how to select a specific SNP for the gene of interest

[Roshan Naik (Dr)]

Dear Sir/Madam,

 

I need you guidance in showing only a specific SNP (based on its reference SNP cluster ID) for the gene of my interest in the genome browser.

 

I clicked on genome browser tab, configure, variation, common SNPs(147) Track Settings. There is an option called Miscellaneous Attributes (dbSNP), but I wish to choose only a particular SNP  and unselect all others for display. I have been looking for all the SNPs for my particular gene locus based on their rs number.

 

I wish to choose only 1 SNP based on their rs number and uncheck all others.

 

But I cannot find  this option under settings. Kiindly guide me.

 

Thanks,

 

Regards,

 

Roshan

 

Dr. Roshan Naik

Research Fellow

59 Nanyang Drive,

Lee Kong Chian School of Medicine (LKC Medicine),

Experimental medicine Building, level 4,

Nanyang Technological University

Singapore 636921

 

 

---

CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents.
Towards a sustainable earth: Print only when necessary. Thank you.

[Luvina Guruvadoo]

Hello Roshan,

Thank you for your question. From my understanding, you would like to display only one SNP in the genome browser display, correct? The best way to do this would be to create a custom track of your SNP, then adjust the genome browser zoom in controls (base level). The zoom in controls are located at the very top of the browser display. I hope this helps.

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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Regards,

Luvina

--

Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu

--

[Roshan Naik (Dr)]

Hello Luvina,

 

Thank you for your response. I added the custom track of my desired SNP: rs7309727.

 

chr12     129470814          129470815             C          1       0    0

 

However, other peaks of POL2  from K562 and GM78 cell line somehow disappear. Please see original image (Image1) and then Image2 after addition of custom track.

 

Kindly guide me.

 

Thanks,

 

Regards,

 

Roshan

[Matthew Speir]

Hi Roshan,

The difference between the two is that in your first image you are zoomed out to where an entire gene is being displayed whereas is the second image you are now zoomed in on a two base pair window.

To display the entire range you have displayed in your first image again, when viewing your tracks in the Genome Browser, enter the position chr12:129,556,271-130,388,212 into the box near the top of the page that says "enter position, gene symbol or search terms" and hit enter.

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.

Matthew Speir
UCSC Genome Bioinformatics Group

--

[Roshan Naik (Dr)]

Hi Matthew,

 

Thank you for your response. I shall try again and hopefully can fix the problem.

 

Regards,

 

Roshan