Embedded Files
SGD's instance of JBrowse, a JavaScript-based genome browser developed by Mitchell Skinner (Skinner et al., 2009, Buels et al., 2016), enables seamless browsing of the yeast genome. In addition to facilitating the browsing of genomic sequences and annotated genomic features, SGD has incorporated many types of published data from genome-wide studies into data tracks. These tracks capture information such as transcription factor binding sites and nucleosome enrichments in order to provide visualization as to how they align with the yeast genome, resulting in an effective method for analysis and for formulating hypotheses. Furthermore, users can upload their own data to analyze or compare with the sequence features and other data tracks.
The tutorials provided below demonstrate the basic navigation of JBrowse, how to view and download data, and how to upload your own data sets into JBrowse tracks. Let us know if there are any published datasets you think should be made available in SGD's JBrowse by sending us an e-mail at sgd-helpdesk@lists.stanford.edu!
Contents
Contents
Overview & Navigation
Downloading & Uploading Information
Webinars
Use Case: S288C Transcriptome
Overview & Navigation Basics
Overview & Navigation Basics
Get started using JBrowse and learn the different ways of exploring the genome. (3:53;created 3/24/16)
Learn the different ways of finding and displaying data tracks from various published data sets. (3:41; created 4/1/16)
Downloading & Uploading Information
Downloading & Uploading Information
A tutorial on how to download the sequence information on JBrowse. (1:02; created 3/30/16)
Find out how to download data tracks and upload your own in JBrowse. (1:56; created 5/10/16)
You can display genes from a YeastMine list in JBrowse! (1:56; created 5/20/16)
Webinars
Webinars
SGD's third webinar covers the basics of JBrowse using the GAL gene system example. (14:33; created 6/2/16)
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