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      PacBio Iso-Seq Workshop Online

Intro to the Workshop
Using Slack in this workshop
Using Zoom in this workshop
Cheat Sheets
Software and Links
Perspective on Bioinformatics/Genomics?
Iso-Seq Library Prep
Logging In
Cluster Computing
Data Reduction
PacBio data
Dr. Liz Tseng
Introduction to PacBio and Iso-Seq
Using the Iso-Seq Application on SMRT Link and BioConda
Richard Kuo
Transcriptome Annotation by Modular Algorithms TAMA
Fairlie Reese
Long-read RNA-seq transcriptomic analysis with TALON and Swan
Download ipython notebook
Conesa Lab
IsoAnnot and IsoAnnotLite
TappAS Install
Hands-on tappAS
Closing thoughts
Github page
Biocore website
Pacific Biosciences website
Conesa lab website

All documentation for the workshop is best viewed from the github.io pages


PacBio Iso-Seq Workshop Online
Aug. 30, 2021, 9 a.m. - Sept. 1, 2021, 5 p.m.
Organizer - Bioinformatics Core
Contact - UC Davis Bioinformatics Core, training.bioinformatics@ucdavis.edu

The Bioinformatics Core is excited to announce a three day workshop on Iso-Seq in partnership with PacBio! With instruction from experienced Core personnel and Iso-Seq analysis experts Dr. Liz Tseng, Principal Scientist at PacBio, and Dr. Ana Conesa, Professor at the University of Florida, this short course will provide a mixture of lectures and hands-on analysis to give participants an overview of the possibilities represented by full length transcript isoform sequencing with Iso-Seq.

Participants will explore experimental design, cost estimation, data generation, and analysis, following Iso-Seq experiments from end to end and learning about several applications of this high quality full length RNA sequence data. Exercises will be performed with provided datasets, using command-line interaction on the Genome Center Compute Cluster.

There are no prerequisites other than basic familiarity with genomic concepts. Some familiarity with the command-line and R is helpful. However, we will dedicate time on the first day to bringing everyone up-to-speed to be able to run the commands needed during this workshop. This workshop will be held remotely over Zoom and Slack, and run from 9:00am to 5:00pm each day.

Industry Sponsors

This workshop is offered in partnership with Pacific Biosciences, and includes instructors and giveaways from PacBio.


Who should attend? … Prior course participants have included faculty, post docs, grad students, staff, and industry researchers.

What are the prerequisites? … There are no prerequisites other than familiarity with general biological concepts and an enthusiasm for learning bioinformatics data analysis. Some familiarity with the command-line and R is desirable. However, we will dedicate time on the first day to bringing everyone up-to-speed to be able to run the commands needed during this workshop.

What do I need in order to participate? … You will need access to a computer with a good internet connection, a recent version of Zoom and Slack installed, and an application that will allow you to ssh into a server (e.g. Putty for windows, or iTerm for Apple). Computational exercises will be performed on a remote server. We can help with setup early on in the workshop. If your department does not allow you to install software on the computer you’ll be using, please contact us ahead of time.

Can I bring my own data? … We will provide experimental datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.

How much does it cost? … The registration fee is $400 for current students, postdocs, staff and faculty at UC campus’ or UC National Labs (LBNL, LANL, LLNL), $500 for other academic or non-profit participants and $600 for other participants. We are pleased to be able to offer three group pricing bundle options for labs with multiple registrants: 15% off registration for groups of 3-5, 25% off registration for groups of 6-10, and custom instructional packages for groups larger than 10. If you are interested in one of these pricing options, please contact us at training.bioinformatics@ucdavis.edu for a custom coupon code.

How do I apply? … All registration is “first-come, first-served”. There is no application process. So, sign up as soon as possible to ensure your place in the workshop.

Where can I find more information, including your policies? … Go to our website (bioinformatics.ucdavis.edu/training/) and check out our FAQ and Policies.


If you have any questions, please don’t hesitate to contact us at training.bioinformatics@ucdavis.edu