GI2012TrackHubsPoster: Difference between revisions

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This page contains links related to the UCSC Genome Browser poster presented by [[User:AngieHinrichs|Angie]] at Biology of Genomes 2012 [http://meetings.cshl.edu/meetings/genome12.shtml])
This page contains links related to the UCSC Genome Browser poster presented by Brian Raney at Genome Informatics 2012 [https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=296])


=Poster: Using the UCSC Genome Browser to evaluate putative genetic variants=
=Remote Data Track Storage for Viewing on the UCSC Genome Browser =


* Files: [[Media:Hinrichs_BoG2012_GBVariants.pptx|.pptx]], [[Media:Hinrichs_BoG2012_GBVariants.pdf|PDF]]
* Files: [[File:BraneyGI2012.pdf]] [[File:BraneyGI2012.pptx]]


==View poster screenshots in the Genome Browser==
= Introduction to Track Data Hubs =
Navigate to this URL to get information about track data hubs, including information about how to set one up, and to register it with the UCSC Genome Browser.


* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=BoG.2012.commonOmimAV Is there an associated phenotype?]
[http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html]
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=BoG.2012.PramefCommonDel How rare is this deletion?]
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=BoG.2012.fictionalVarPseudogeneRegPeak Novel variant: what's in the neighborhood?]
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=BoG.2012.funWith1kG Decoding the VCF w/phased genotypes display]
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=BoG.2012.dbSNPbabyBathwater dbSNP: Not just polymorphisms]


==1000 Genomes Phase 1 v3 integrated variants (May 2012) used in the poster==
=How to get help=
Thanks to the [http://www.1000genomes.org/ 1000 Genomes Project] for making these data available:
[ftp://ftp.ncbi.nih.gov/1000genomes/ftp/release/20110521/ ftp://ftp.ncbi.nih.gov/1000genomes/ftp/release/20110521/]
To view a chromosome's phased genotype calls in the browser, right-click to copy the corresponding link ending in ".genotypes.vcf.gz" and then use that as the bigDataUrl parameter as described here: [http://genome.ucsc.edu/goldenPath/help/vcf.html http://genome.ucsc.edu/goldenPath/help/vcf.html]
 
==How to get help==
* Search for answers in our mail list archives: [http://genome.ucsc.edu/contacts.html http://genome.ucsc.edu/contacts.html]
* Search for answers in our mail list archives: [http://genome.ucsc.edu/contacts.html http://genome.ucsc.edu/contacts.html]
* Email a new question to our actively monitored list [mailto:genome@soe.ucsc.edu genome@soe.ucsc.edu]
* Email a new question to our actively monitored list [mailto:genome@soe.ucsc.edu genome@soe.ucsc.edu]
* OpenHelix's free training materials: [http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml]
* OpenHelix's free training materials: [http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml]


==Other posters about the UCSC Genome Browser==
=Other posters and presentations about the UCSC Genome Browser, or by related groups=
 
[[Presentations]]


* Visually integrating genomic data in the UCSC Genome Browser. Hinrichs AS ''et al.'' HGV 2011 [[HGV2011|genomewiki page]]  [[Media:HGV2011_GenomeBrowser.pptx|.pptx]], [[Media:HGV2011_GenomeBrowser.pdf|PDF]]
[[Category:Technical FAQ]]
* UCSC Genome Browser Data Hubs. Zweig AS ''et al.'' Biology of Genomes, 2011 [http://users.soe.ucsc.edu/~ann/BoG2011.pdf PDF]
[[Category:Assembly/Track Hubs]]
* Genome-wide ENCODE Data at UCSC. Rosenbloom KR ''et al.'' ASHG, 2010. [[Media:ENCODE_ASHG2010.ppt|PPT]]
* UCSC Genome Browser Tool Suite. Hinrichs AS ''et al.'' Genomics of Common Disease, 2008: [[Media:UCSC_Genome_Browser_GCD_2008.ppt|.ppt]], [[Media:UCSC_Genome_Browser_GCD_2008.pdf|PDF]]

Latest revision as of 21:08, 23 April 2013

This page contains links related to the UCSC Genome Browser poster presented by Brian Raney at Genome Informatics 2012 [1])

Remote Data Track Storage for Viewing on the UCSC Genome Browser

Introduction to Track Data Hubs

Navigate to this URL to get information about track data hubs, including information about how to set one up, and to register it with the UCSC Genome Browser.

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

How to get help

Other posters and presentations about the UCSC Genome Browser, or by related groups

Presentations

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