This is an archive of our previous webinars. If you are interested in attending a live webinar, visit our webinar registration page for a listing of upcoming sessions. If you have any questions on the topics below, feel free to contact us and we will be happy to schedule a Q&A session for you.
This webinar is for everyone who is interested in learning the basics of sequence data management and how to start analyzing sequence data, using the workflows for the three most common NGS experiment types: ChIP-Seq, RNA-Seq, and DNA-Seq. It also covers pathway analysis and data exploration in the highly-interactive genome browser in Avadis NGS.
This webinar will focus only on the RNA-Seq workflow of Avadis NGS. It covers the main steps of analyzing RNA-Seq data, including gene expression analysis, transcript expression analysis, SNP detection, and how to discover novel genes and novel splice junctions using Avadis NGS.
This webinar will focus only on the DNA-Seq workflow of Avadis NGS. Register for this webinar if you are interested in learning more about detecting and predicting the effects of SNPs and InDels, as well as finding larger structural variations and translocations.
This webinar will focus only on the ChIP-Seq workflow of Avadis NGS. We will explain the various peak finding algorithms available in Avadis NGS and the GADEM motif discovery algorithm. In addition, the webinar will also cover the downstream analysis options available in Avadis NGS, including gene ontology analysis and pathway analysis.
Genome Browser Highlights
Did you know that Avadis NGS has an embedded, feature-rich Genome Browser? This webinar will show you how to the best use of all its features, as well as how to customize it for better interaction with your data and improved visualization of your analysis results to use in publications.
Analyzing Cancer Data with Avadis NGS
This webinar focuses on the analysis of NGS data in the context of cancer biology using the various analysis and biological interpretation tools available in the RNA-Seq and DNA-Seq workflows of Avadis NGS. We will discuss differential gene expression, alternate transcript isoforms, somatic and germline SNPs, and aneuploidies, which are all commonly studied in various forms of cancer.
Pathway Analysis in Avadis NGS
Many NGS analyses like differential expression, peak finding, and SNP effect analysis, result in a list of genes. Avadis NGS provides several downstream tools like GO analysis, GSEA, and pathway analysis for further exploration of these entity lists. This webinar is focused on the pathway analysis features in Avadis NGS. We will briefly describe the packaged interaction databases that contain ~2 million interactions derived using Strand's proprietary Natural Language Processing (NLP) algorithms on 16 million Medline abstracts. Watch the recording of this webinar to learn how to effectively query the interaction databases to detect relationships between entities of interest, how to create pathways from the interaction database, how to import curated pathways from external sources such as Reactome and Cancer Cell Map, and how to use the saved pathways in data interpretation.
Quality Control in Avadis NGS
Watch the recording of this webinar if you would like to find out more about quality control of NGS data and the QC features on offer in Avadis NGS. The webinar helps you understand how you can perform various Quality Control (QC) steps in Avadis NGS to make sure you retain only the best reads for the later analysis steps. It covers the various QC visualizations available in Avadis NGS that allow you to efficiently determine how good (or bad) the reads in your data are. Following that, we demonstrate how to use the available QC filtering steps to remove bad quality reads.
Analyzing Whole Genome Experiments
This webinar focuses on the scalability and performance of Avadis NGS when importing and analyzing large data sets. It includes details on identifying and analyzing SNPs and SVs and their effects on the transcript. We will be using a Yoruba high coverage whole genome sample for this demonstration.
Small RNA Analysis in Avadis NGS 1.3
Avadis NGS already has comprehensive analysis pipelines for RNA-Seq, DNA-Seq and ChIP-Seq data. The next version of Avadis NGS comes with a new pipeline for the analysis of small RNA data as a separate experiment type. Watch the recording of this webinar, to know more about what’s new in Avadis NGS 1.3. In this webinar, we will describe the new small RNA read aligner, small RNA specific QC and filtering steps, quantification, and differential expression method. Since annotations for small RNA species are usually incomplete, we will show you how to detect and classify novel small RNAs. In addition, we will also show you how to use the multiple miRNA target prediction databases to identify target genes on which downstream analysis can be performed.
Alignment of raw reads in Avadis NGS 1.3 using COBWeb
The upcoming release of Avadis NGS 1.3 provides support for aligning raw reads for small RNA, ChIP-Seq and DNA-Seq analysis. The alignment algorithm integrated with Avadis NGS is a new proprietary algorithm based on the Burrows Wheeler Transform. We have christened our new algorithm COBWeb - a metaphor for strength in simplicity as well as a reflection of multi-scale design, the attributes that have inspired the algorithm. COBWeb is optimized to handle both short and long reads and is capable of handling an arbitrary number of gaps and mismatches, so you won’t need to search for other aligners, which are often limited to either a specific class of reads or alignment characteristics.
Support for MiSeq Data in Avadis NGS
Avadis NGS 1.3 provides special support for analyzing data generated by MiSeq™ sequencers. In this webinar, we will describe how the data in a MiSeq generated "run folder" is automatically loaded into the Avadis NGS software during small RNA alignment and DNA variant analysis. This is especially helpful in processing the large number of files generated when the TruSeq™ Amplicon Kits are used. We will describe how to use the QC steps of Avadis NGS to check if the amplicons have sufficient coverage in all the samples. Regions with unexpected coverages can easily be identified using the new region list clustering feature. We will illustrate how to use the Find Significant SNPs feature to quickly identify high-confidence SNPs present in a majority of the samples, rare variants etc.
Analysis of Ion Torrent Data in Avadis NGS
The Avadis NGS includes a new aligner - COBWeb - that is fully capable of aligning the long, variable-length reads generated by Ion Torrent sequencers. In this webinar, we will show the pre-alignment QC plots and illustrate how they can be used to set appropriate alignment parameters for aligning Ion Torrent reads. For users who choose to import the BAM format files generated by the Ion Torrent Server, we will describe the steps needed for importing amplicon sequencing data into Avadis NGS. Users of the Ion AmpliSeq™ Cancer Panel will learn how to easily import the targeted mutation list and verify the genotype call at the mutation sites. We will illustrate how to use the Find Significant SNPs feature to quickly identify high-confidence SNPs present in a majority of the samples, rare variants etc.
Find Significant SNPs using Avadis NGS
SNP verification and prioritization is one of the most time consuming tasks in variant analysis. Avadis NGS 1.3 includes numerous changes to make end-to-end SNP analysis easy and intuitive. The SNP detection algorithm has been enhanced to improve accuracy. In this webinar, we will show you the new "Find Significant SNPs" analysis workflow in Avadis NGS 1.3. This workflow supports multiple experimental setups and can be used to quickly identify population-specific variants, somatic mutations, and tumor-specific markers via an intuitive graphical user interface.
RNA-Seq Alignment in Avadis NGS
The next version of Avadis NGS features enhancements to the RNA-Seq analysis workflow, namely an extension of the COBWeb alignment algorithm to enable alignment of RNA-Seq reads. Reads obtained from single/paired-end libraries or directional RNA-Seq protocols can be imported into the new RNA-Seq Alignment experiment. This workflow allows users to perform alignment against a transcript model and additionally against the genome.
Local Realignment and Base Quality Score Recalibration
Avadis NGS is our solution to the analysis of next generation sequencing data and features comprehensive support for end-to-end DNA-Seq analysis. The DNA-Seq workflow includes algorithms and general purpose tools for detecting and predicting the effects of SNPs and InDels, as well as for finding larger structural variations. The workflow in our upcoming release will be extended to include support for (i) base quality score recalibration to account for inaccuracies and biases in base quality scores reported by sequencers, and (ii) local realignment to handle multiple mismatches in alignment near InDels. In this webinar, we will describe our approach for base quality score recalibration and local realignment and demonstrate how these steps can help to decrease false positive variant calls in the downstream analysis.