The Ontario Genomics Institute (OGI) and The Centre for Applied Genomics (TCAG) hosted a 1 hour web conference/webinar about Savant - a visual analytics platform for genomic data. Savant improves upon existing genome browsers in interface design and data presentation. Most importantly, Savant is unique in its ability to perform complex analytics on the visualized data in real-time, complements of a rich plugin framework.
The webinar covered:
Basics of the interface:- Loading tracks
- Navigation
- Bookmarking
- Table View
- Data Selection
Visualizing Next generation sequencing data:- Visualizing read alignments
- Identifying point and structural mutations by eye (SNPs, indels, CNVs)
- Assessing the quality of variant predictions
Plug-in framework:- Browsing and installing plug-ins
- Opening UCSC tracks directly
- Identifying SNPs automatically using realtime SNP Finder
Link to the webinar recording:
http://ogi.acrobat.com/p1k1q8c51qh/
For a link to the Savant genome browser:
http://genomesavant.com/Responses to questions asked in the Savant webinar on May 19th 2011Q: Can you copy sequence from a genome track (for use in BLAST, for example)?
A: Yes. You can display the sequence using the Table View module, and copy from there too.
Q: What's the format for the bookmarks? That seems like a great feature.
A: Bookmarks can be loaded from a BED file or from a tab-delimited text file where the first three fields are chromosome, then start position, then end position.
Q: What are the checkboxes in the Table View for - are they clickable?
A: Checkboxes are used to denote the values of Boolean (i.e. true or false) fields. A clicked box represents true. Since the Table View corresponds to the underlying data file, these checkboxes are not changeable by clicking.
Q: Can you adjust colors to your preferences?
A: Yes, color settings can be changed through Edit -> Preferences menu or through track-specific settings shown in the upper-right corner of active tracks.
Q: Is it possible to export SNP's [found by the SNP Finder Plugin] that are novel only or cause stop codons for example?
A: No, not currently. A project that we're working on (called MedSavant for now) might better suit this need. Stay tuned...
Q: Is there any web based tutorial to learn SAVANT and subsequent analysis?
A: Many tutorial videos are posted on our website,
www.savantbrowser.com, in the Documentation section.
Q: Is there any difference between Mac and Windows version of SAVANT?
A: Besides aesthetics, there are only very minor differences in the functionalities of Savant on the various platforms. Support is best on Mac and Windows.
Q: For chromatin immunoprecipitations, it would be nice to get an output of the different types of features that come out. Is it possible to generate a list of hits that overlap with e.g. ORFs, replication origins, repetetive elements etc?
A: Stay tuned to our progress on MedSavant...
Q: Can you use Savant for RNAseq analyses?
A: Yes, as long as you can provide alignments to a reference genome (in the form of BAM files). Our Cufflinks Plugin helps to determine transcript abundances for such datasets.
