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Avadis NGS April 6, 2011
News & Updates

Tutorials for RNA-Seq and ChIP-Seq

We have created do-it-yourself tutorials, bundled with sample data, for the RNA-Seq and ChIP-Seq analysis workflows in Avadis NGS. You can download the ChIP-Seq tutorial (NRSF) or the RNA-Seq tutorial (Jurkat) packaged with sample data from the Download section of our website. The tutorial on DNA-Seq will be available soon.

New script to determine read coverage of selected regions

We have added a new script to determine read coverage of selected regions to our online Scripts Library, providing you an additional method to get the most out of your sequence data. The script allows you to identify the number of overlapping reads for each region in a given region list. For example, once you have identified the exonic regions in your data (using Script #1 in our library), you can use this script to identify the exons that are not adequately covered by exome sequencing.

Video tutorials on how to inspect quality of sequence data

One important feature of Avadis NGS is that it allows you to check the quality of your sequencing data before you begin downstream analysis. The Quality Inspection workflow helps you identify bad reads on the basis of base quality, alignment status, alignment score, and mate status. Then, numerous filters allow you to remove reads that may corrupt your analysis. Watch our new series of video tutorials on those quality inspection features to learn more.

Feature Highlight

Use R functionality in Avadis NGS to identify differentially expressed genes

The Avadis NGS R Editor lets you load and run R scripts on your experiment data as part of your RNA-Seq workflow. Just follow the simple instructions on our website on how to download the free R software and other requirements to get started.

The first script we have provided for you is the DESeq R script, which allows you to identify differentially expressed genes between two experiment conditions.

Upcoming Events

New webinars in April on the analysis of DNA-Seq data and more!

We have scheduled four webinars for you to attend in April, including a new presentation focusing on the DNA-Seq workflow in Avadis NGS. Register for this 45-minute DNA-Seq webinar to learn about detecting and predicting the effects of SNPs and InDels, as well as finding larger structural variations and translocations.

There will also be two introductory webinars, giving you an overview of the three experiment workflows. In addition, there will be another session focusing on the RNA-Seq workflow, including details on differential gene and transcript expression analysis, as well as detecting alternative and novel splice junctions and genes. Register for free today to attend one of these webinars!

Date/Time Pacific Daylight Time
(San Francisco)
Eastern Daylight Time
(New York)
Central European Time
China Time
April 7th
-- -- 11 AM 5 PM
April 12th
-- -- 11 AM 5 PM
April 13th
8 AM 11 AM 5 PM --
April 28th
8 AM 11 AM 5 PM --

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.

Coming Soon . . .

"Create your own genome" video tutorial

The Avadis NGS software package includes the genome annotations for numerous organisms, which can be downloaded within the software. However, if you are researching an organism that is not currently in the Avadis NGS package, the Create option in the Annotations Manager will lead you through the annotations assembly. The process of creating annotations isn't the most straightforward endeavor because it requires pulling together a lot of data files from various sources like UCSC, Ensemble and RefSeq (depending on your organism) -- but with the help of our new video tutorial, it should become a lot easier. We will post it online soon.

We will be continually adding new annotations to our server for you to download via the Annotation Manager, including Arabidopsis thaliana and C. elegans, which will be available soon. Ask our support team if the annotations for your organism of interest will be supported soon, and perhaps it will be bumped up in the queue!

Just Ask!

Thanks to all who have given us great feedback and responses, both directly and indirectly through online forums. We pass all your comments, requests and questions to our scientists and engineers to ensure that we continually improve the solutions Avadis NGS offers you. Please keep your comments coming!

- The Avadis NGS Team

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