https://genomewiki.ucsc.edu/index.php?title=BoG2012VariationPoster&feed=atom&action=historyBoG2012VariationPoster - Revision history2024-03-28T18:46:13ZRevision history for this page on the wikiMediaWiki 1.38.4https://genomewiki.ucsc.edu/index.php?title=BoG2012VariationPoster&diff=19775&oldid=prevAngieHinrichs: Page with links to poster source, session links, 1kG data used, help pages etc.2012-05-07T15:59:58Z<p>Page with links to poster source, session links, 1kG data used, help pages etc.</p>
<p><b>New page</b></p><div>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])<br />
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=Poster: Using the UCSC Genome Browser to evaluate putative genetic variants=<br />
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* Files: [[Media:Hinrichs_BoG2012_GBVariants.pptx|.pptx]], [[Media:Hinrichs_BoG2012_GBVariants.pdf|PDF]]<br />
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==View poster screenshots in the Genome Browser==<br />
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* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=BoG.2012.commonOmimAV Is there an associated phenotype?]<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=BoG.2012.PramefCommonDel How rare is this deletion?]<br />
* [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?]<br />
* [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]<br />
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=BoG.2012.dbSNPbabyBathwater dbSNP: Not just polymorphisms]<br />
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==1000 Genomes Phase 1 v3 integrated variants (May 2012) used in the poster==<br />
Thanks to the [http://www.1000genomes.org/ 1000 Genomes Project] for making these data available:<br />
[ftp://ftp.ncbi.nih.gov/1000genomes/ftp/release/20110521/ ftp://ftp.ncbi.nih.gov/1000genomes/ftp/release/20110521/]<br />
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]<br />
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==How to get help==<br />
* Search for answers in our mail list archives: [http://genome.ucsc.edu/contacts.html http://genome.ucsc.edu/contacts.html]<br />
* Email a new question to our actively monitored list [mailto:genome@soe.ucsc.edu genome@soe.ucsc.edu]<br />
* OpenHelix's free training materials: [http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml]<br />
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==Other posters about the UCSC Genome Browser==<br />
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* 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]]<br />
* UCSC Genome Browser Data Hubs. Zweig AS ''et al.'' Biology of Genomes, 2011 [http://users.soe.ucsc.edu/~ann/BoG2011.pdf PDF]<br />
* Genome-wide ENCODE Data at UCSC. Rosenbloom KR ''et al.'' ASHG, 2010. [[Media:ENCODE_ASHG2010.ppt|PPT]]<br />
* 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]]</div>AngieHinrichs