RE: UCSC Genome Browser

[Joseph Califano]

Name of assembly: hg19

Name of track: TGCA_HNSC_NG_RNA

Exact location of viewing: chr5:67,585,611-67,587,752

Web browser: Chrome (v35.0), OS- Windows 7

To whom it may concern:

I have a question regarding the Genome Browser.   I am seeking to view TCGA data for Head and Neck tumors, and when querying our gene of interest I am interested in looking at the specific expression of an exon, I am unable to view the tracks in any display except for in the "Dense" one line display even when I request for other display modes such as squish, pack or full. 

I noted that in your help manual that it says that "When the number of lines within a requested track location exceeds 250, the track automatically defaults to a more tightly-packed display mode."  When I look at other tracks such as TCGA_LUSC_RNA, I am able to view in the pack mode, and more importantly view normal samples and compare them to tumor samples. 

I am wondering if there is anyway to view the TGCA_HNSC_NG_RNA track in Pack mode as above.  I have tried zooming in quite close to the exon of interest (<1000 bp) but this did not work.  Is there a way to perhaps selected a subset of samples to view fewer at one time?

Your help is much appreciated,

Joe Califano

Joseph Califano, M.D.

Professor

Department of Otolaryngology-Head and Neck Surgery

Johns Hopkins Medical Institutions

1550 Orleans Street, Room 5N.04

Baltimore, Maryland 21231

 

Johns Hopkins Head and Neck Surgery

Milton J. Dance Head and Neck Center

Greater Baltimore Medical Center

6569 N. Charles Street

Physicians Pavilion West, Suite 401

Baltimore, Maryland 21204

 

clinical office 443-849-8940

clinical fax 443-849-8965

administrative office 410-955-6420

laboratory 410-502-2692

laboratory fax 410-614-1411

 

[Luvina Guruvadoo]

Hello Joseph,

Thanks for your question, but I was unable to locate these tracks on our main site (http://genome.ucsc.edu). Are you viewing these tracks on a mirror site such as https://cgwb.nci.nih.gov/cgi-bin/hgTracks? If so, we suggest you contact the folks at the CBIIT/National Cancer Institute who maintain that site.

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.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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