Register for our Iso-Seq webinars below:
In this webinar we will present the recent Iso-Seq template preparation protocol updates for creating full-length cDNAs and discuss considerations for experimental design.
Topics Covered
- Why full-length transcript sequences matter
- Overview of Iso-Seq template preparation methods
- Updates to protocol allowing for sequencing of transcripts up to ˜10 kb
- Methods for size fractionation
- Applications of the Iso-Seq method
- Targeted transcript sequencing
- Normalization
Who should attend:
Biologists and technicians who are running Iso-Seq experiments and anyone who is interested in learning more about using long read sequencing to study full-length transcripts.
Recommended Pre-reading:
- General information on Isoform Sequencing
- User Bulletin - Guidelines for Preparing cDNA Libraries for Isoform Sequencing (Iso-Seq™)
Click on your preferred time below to register:
Presenter Biography
Tyson A. Clark, Ph.D.
Senior Manager, Next Generation Applications and Technologies
In 2002, Tyson received his doctorate degree in Molecular Biology from the University of California, Santa Cruz. He was a pioneer in the use of microarrays to study alternative splicing events on a genome-wide scale. After working in the gene expression space at Affymetrix, Tyson joined Pacific Biosciences in 2009. His energy is focused on the development of new applications for use on the PacBio RS II.
In this webinar we will demonstrate how to run the Iso-Seq bioinformatics software pipeline that is part of PacBio's SMRTAnalysis software suite. Both the web portal interface (SMRT Portal) and the command line version will be introduced. In addition, we will be using the community version of Iso-Seq (pbtranscript-tofu) and other community tools to perform additional analyses.
Topics Covered
- Iso-Seq Bioinformatics Pipeline*:
- running from SMRTPortal web interface
- running from command line
- interpreting Iso-Seq output results
- troubleshooting
- Beyond Iso-Seq**:
- visualizing isoforms
- comparing against reference transcript annotations
- look for fusion gene candidates
- open reading frame prediction
- and more...
* Demonstrated using the latest official Iso-Seq protocol from SMRTAnalysis 2.3
** Enabled through use of community tools
Who should attend:
Bioinformaticians interested in running and analyzing PacBio Iso-Seq datasets. Familiarity with Unix and Python is expected.
Recommended Pre-reading::
Click on your preferred time below to register:
Presenter Biography
Elizabeth Tseng
Senior Staff Scientist, Pacific Biosciences
Elizabeth obtained her doctorate degree in Computer Science & Engineering from the University of Washington in 2012. Her thesis work focused on the computational discovery of bacterial non-coding RNAs and gut microbiome. After joining PacBio, she decided to give prokaryotes a break and now supports and develops eukaryotic transcriptome-related collaborations.