[rat-forum] Announcing the official release of RGD's JBrowse genome browser

Smith, Jennifer jrsmith at mcw.edu
Wed Feb 25 10:43:28 CST 2015


RGD is pleased to announce the official release of our JBrowse Genome Browsers for Rat<http://rgd.mcw.edu/jbrowse/?data=data_rgd5&loc=Chr5%3A171596917..171780189&tracks=ARGD_curated_genesOnly%2CARGD_curated_genes%2CRNAseq_Lazar_SS_H1%2CCongenicStrains%2CAQTLS&highlight=>, Human<http://rgd.mcw.edu/jbrowse/?data=data_hg19&loc=Chr11%3A73666568..73728733&tracks=ARGD_curated_genes%2CCardiovascularDiseasesGenes%2CHapten%2CProvitamin%2CRatSyntenyBlock%2CMouseSyntenyBlock&highlight=> and Mouse<http://rgd.mcw.edu/jbrowse/?data=data_mm37&loc=Chr7%3A107607349..107654498&tracks=ARGD_curated_genesOnly%2CARGD_curated_genes%2CCardiovascularDiseasesGenes%2CProvitamin%2CEpitope%2CRat34SyntenyBlock%2CHuman37SyntenyBlock&highlight=>!  Similar to GBrowse in functionality, although quite different in "look and feel", the JBrowse genome browser is a faster and more dynamic browser than the legacy GBrowse.  Plus, while all of the data available in GBrowse is also available in JBrowse, the latter browser contains additional data, such as RNA-Seq BAM alignment tracks, not available in GBrowse.  Since the developer of both browsers, the Generic Model Organism Database (GMOD), is deprecating the GBrowse browser in favor of the new JBrowse, RGD will be moving toward exclusive use of the new browser over time.  In the meantime, both browsers are available from the RGD home page<http://rgd.mcw.edu/> and the "Genome Tools<http://rgd.mcw.edu/wg/tool-menu>" page.

To get started with JBrowse, click any of these links:

Rat JBrowse genome browser<http://rgd.mcw.edu/jbrowse/?data=data_rgd5&loc=Chr5%3A171596861..171780133&tracks=ARGD_curated_genesOnly%2CARGD_curated_genes%2CRNAseq_Lazar_SS_H1%2CCongenicStrains%2CAQTLS&highlight=>
Human JBrowse genome browser<http://rgd.mcw.edu/jbrowse/?data=data_hg19&loc=Chr11%3A73666551..73714250&tracks=ARGD_curated_genes%2CCardiovascularDiseasesGenes%2CHapten%2CProvitamin%2CRatSyntenyBlock%2CMouseSyntenyBlock&highlight=>
Mouse JBrowse genome browser<http://rgd.mcw.edu/jbrowse/?data=data_mm37&loc=Chr7%3A107607351..107654500&tracks=ARGD_curated_genesOnly%2CARGD_curated_genes%2CCardiovascularDiseasesGenes%2CProvitamin%2CEpitope%2CRat34SyntenyBlock%2CHuman37SyntenyBlock&highlight=>

Need help getting started with JBrowse?  RGD has produced extensive help documentation to give you a "leg up" whether you are looking for an overview of the browser<http://rgd.mcw.edu/wg/help3/tools/rgd-genome-browsers/the-rat-jbrowse-genome-browser>, want to see a side-by-side comparison of GBrowse and JBrowse<http://rgd.mcw.edu/wg/help3/tools/rgd-genome-browsers/gbrowse-to-jbrowse-comparison>, or need help with a particular type of JBrowse track<http://rgd.mcw.edu/wg/help3/tools/rgd-genome-browsers/the-rat-jbrowse-genome-browser/more-about-jbrowse-tracks>.

If you have any questions, comments or suggestions regarding JBrowse (or anything else to do with RGD, our data, our tools or our website), please do not hesitate to contact us<http://rgd.mcw.edu/contact/index.shtml>!

The RGD team





If you prefer copy and paste URLs into your web browser, here is a list of the links in this email:

The RGD Home Page:
http://rgd.mcw.edu

RGD Genome Tools page:
http://rgd.mcw.edu/wg/tool-menu

Rat JBrowse:
http://rgd.mcw.edu/jbrowse/?data=data_rgd5&loc=Chr5%3A171596861..171780133&tracks=ARGD_curated_genesOnly%2CARGD_curated_genes%2CRNAseq_Lazar_SS_H1%2CCongenicStrains%2CAQTLS&highlight=

Human JBrowse:
http://rgd.mcw.edu/jbrowse/?data=data_hg19&loc=Chr11%3A73666551..73714250&tracks=ARGD_curated_genes%2CCardiovascularDiseasesGenes%2CHapten%2CProvitamin%2CRatSyntenyBlock%2CMouseSyntenyBlock&highlight=

Mouse JBrowse:
http://rgd.mcw.edu/jbrowse/?data=data_mm37&loc=Chr7%3A107607351..107654500&tracks=ARGD_curated_genesOnly%2CARGD_curated_genes%2CCardiovascularDiseasesGenes%2CProvitamin%2CEpitope%2CRat34SyntenyBlock%2CHuman37SyntenyBlock&highlight=

RGD JBrowse Help pages:
http://rgd.mcw.edu/wg/help3/tools/rgd-genome-browsers/the-rat-jbrowse-genome-browser
http://rgd.mcw.edu/wg/help3/tools/rgd-genome-browsers/gbrowse-to-jbrowse-comparison
http://rgd.mcw.edu/wg/help3/tools/rgd-genome-browsers/the-rat-jbrowse-genome-browser/more-about-jbrowse-tracks

Contact Us:
http://rgd.mcw.edu/contact/index.shtml



-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.mcw.edu/pipermail/rat-forum/attachments/20150225/ec023029/attachment.html 


More information about the rat-forum mailing list