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July 5, 2011 |
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News & Updates
BIOBASE Genome TraxTM annotations are now integrated in Avadis® NGS
With the release of version 1.2.2 on 30 June 2011, BIOBASE Genome Trax annotations are now available from within Avadis NGS. Existing users can simply update their installation to the new version, which will open a demo RNA-Seq experiment, containing Alzheimer's disease tissue and normal tissue samples, illustrating this new feature. This demo project can also be explored with a free evaluation license.
Export Projects and Sets of Experiments
In Avadis NGS version 1.2.2 you can now also export entire projects, or sets of experiments, in the .tar format, to archive them outside the application. Should you require any of the exported projects again at a later date, they can easily be re-imported. Find out what else is new in version 1.2.2 here.
Video Tutorial on Adding Chromosome Aliases
You created an experiment and loaded your samples, but can't see any reads in the genome browser? This is most likely due to the fact that your alignment program has assigned chromosome names to your reads, that Avadis NGS cannot recognize. Watch this video and find out how you can identify the chromosome names in your sample and add these chromosome aliases in the Annotations Manager in order to be able to see those reads.
Filter SNPs across multiple samples
If you are looking for SNPs in a large numbers of samples the latest script (Script #9) in our online Script Library allows you to filter your SNP results according to zygosity, as well as other characteristics, in one simple operation. This will narrow down the number of SNPs of interest to your research and creates a new SNP results list that can be used for further analyses, such as SNP Effect Analysis.
Feature Highlight
Visualize Base Quality
Want to QC your data for base quality to allow you to make a more informed choice on what reads to remove before analysis? Use Script #8 in our online Script Library, to visualize the average base quality values of your reads and filter them accordingly, using the Filter by Read Metrics feature in Avadis NGS.
Below: Average base quality of reads in a Yoruba whole genome sample as visualized in Avadis NGS
Upcoming Events
Free Avadis NGS Webinars in July!
Find out more about Avadis NGS and how it can benefit your research by attending one of our free webinars. You can register here for one of these sessions:
Subject
Date |
Pacific Daylight Time
(San Francisco) |
Eastern Daylight Time
(New York) |
Central European Time
(Berlin) |
China Time
(Beijing) |
RNA-Seq
13 July 2011 |
8 AM |
11 AM |
5 PM |
-- |
Genome Browser
14 July 2011 |
-- |
-- |
11 AM |
5 PM |
Analyzing
Cancer Data
19 July 2011 |
-- |
-- |
11 AM |
5 PM |
ChIP-Seq
21 July 2011 |
-- |
-- |
11 AM |
5 PM |
DNA-Seq
26 July 2011 |
-- |
-- |
11 AM |
5 PM |
Pathway Analysis
27 July 2011 |
8 AM |
11 AM |
5 PM |
-- |
Whole Genome
Analysis
26 July 2011 |
-- |
-- |
11 AM |
5 PM |
As always, if you can't make it for one of these dates you also have the option to request a private webinar session by selecting "I would prefer a private session for my organization" from the Preferred Date menu on the registration page.
Just Ask!
Let us know what you think about Avadis NGS! Using your feedback we can make sure that we provide the best possible solution for your NGS analysis pipeline, by including your feature request in our next release, or providing you with the right scripts to accomplish your research, just like the scripts you read about here.
- The Avadis NGS Team
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