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]) | |||
=Poster: Using the UCSC Genome Browser to evaluate putative genetic variants= | |||
* Files: [[Media:Hinrichs_BoG2012_GBVariants.pptx|.pptx]], [[Media:Hinrichs_BoG2012_GBVariants.pdf|PDF]] | |||
==View poster screenshots in the 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/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== | |||
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] | |||
* 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] | |||
==Other posters about the UCSC Genome Browser== | |||
* 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]] | |||
* UCSC Genome Browser Data Hubs. Zweig AS ''et al.'' Biology of Genomes, 2011 [http://users.soe.ucsc.edu/~ann/BoG2011.pdf PDF] | |||
* 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]] | |||
Revision as of 01:30, 25 August 2012
This page contains links related to the UCSC Genome Browser poster presented by Angie at Biology of Genomes 2012 [1])
Poster: Using the UCSC Genome Browser to evaluate putative genetic variants
View poster screenshots in the Genome Browser
- Is there an associated phenotype?
- How rare is this deletion?
- Novel variant: what's in the neighborhood?
- Decoding the VCF w/phased genotypes display
- dbSNP: Not just polymorphisms
1000 Genomes Phase 1 v3 integrated variants (May 2012) used in the poster
Thanks to the 1000 Genomes Project for making these data available: 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
How to get help
- Search for answers in our mail list archives: http://genome.ucsc.edu/contacts.html
- Email a new question to our actively monitored list genome@soe.ucsc.edu
- OpenHelix's free training materials: http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml
Other posters about the UCSC Genome Browser
- Visually integrating genomic data in the UCSC Genome Browser. Hinrichs AS et al. HGV 2011 genomewiki page .pptx, PDF
- UCSC Genome Browser Data Hubs. Zweig AS et al. Biology of Genomes, 2011 PDF
- Genome-wide ENCODE Data at UCSC. Rosenbloom KR et al. ASHG, 2010. PPT
- UCSC Genome Browser Tool Suite. Hinrichs AS et al. Genomics of Common Disease, 2008: .ppt, PDF
