[Tony Roscioli]

Dear UCSC genome browser team

 

I have a very specific question regarding upload of point or interval data by BED files to the UCSC.

 

I am comfortable doing this on the browser itself but wondered if an interval could be demonstrated on a karyogram on the site which contains all chromosomes?

 

The utility of this would for example be for homozygosity mapping intervals.

 

 

I’d be interested if you have a solution or if you could point me in the right direction

 

 

Thanks

 

 

Tony

 

 

Dr Tony Roscioli FRACP PhD

Staff Specialist in Clinical Genetics, Sydney Children's Hospital

Visiting Scientist, the Garvan Institute

Senior Lecturer, UNSW

 

Tel: +61 2 9382 1704

 

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[Steve Heitner]

Hello, Tony.

We have a Genome Graphs tool (http://genome.ucsc.edu/cgi-bin/hgGenome) that should do what you’re trying to accomplish.  Please see the User’s Guide at http://genome.ucsc.edu/goldenPath/help/hgGenomeHelp.html to help you get started.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  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.

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Steve Heitner
UCSC Genome Bioinformatics Group

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[Song, Qing]

I have downloaded the GWAS catalog dataset (human hg19) from your site, but I cannot find a unique identifier for each project or each snp to link your dataset back to the dbGaP project ID. Is there a way to link them? Thank you. Qing

[Jonathan Casper]

Hello Qing,

Thank you for your question about linking GWAS Catalog IDs to dbGaP projects. Unfortunately, it does not look like there is an easy and automated way to link from one to the other. The researchers at GWAS Catalog or dbGaP might have some suggestions.

One of our engineers offers the following comments:

I was hoping that PubMed IDs could be used to match them up, but it doesn't look like it. Our gwasCatalog table has a pubMedID column with numeric PubMed IDs. dbGAP project pages include links to PubMed (scroll down to "Selected publications'"). But... they're not necessarily the same. For example, gwasCatalog has some variants from a 2012 study with pubmed 23128233. You can read it in PMC: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491803/ -- search for dbGAP and it lists a couple project numbers. But the pubmed links for http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000130.v1.p1 and phs000345.v1.p1 are for older publications... ah, the 2012 study in gwasCatalog is a meta-analysis.

If you are only pursuing this link for a few studies, the method described above of looking up dbGaP project numbers in the associated PubMed article might work for you. You might also find the Association Results Browser from NCBI helpful - you can search by gene or position and limit the search results to those with dbGaP as a source.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums 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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Jonathan Casper
UCSC Genome Bioinformatics Group

On Fri, Jun 20, 2014 at 3:09 PM, Song, Qing <qs...@msm.edu> wrote:

I have downloaded the GWAS catalog dataset (human hg19) from your site, but I cannot find a unique identifier for each project or each snp to link your dataset back to the dbGaP project ID. Is there a way to link them? Thank you. Qing

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