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      PacBio Iso-Seq Workshop Online

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Introduction
Intro to the Workshop
Schedule
Support
Using Slack in this workshop
Using Zoom in this workshop
Cheat Sheets
Software and Links
Talks
Perspective on Bioinformatics/Genomics?
Iso-Seq Library Prep
Command Line Interface
Logging In and Transferring Files
Intro CLI
Advanced CLI
Advanced CLI Challenge Solutions
Clusters and Modules
Data Reduction
PacBio data
Dr. Liz Tseng
SMRT Sequencing - How it Works
Using the Iso-Seq Application on SMRT Link and BioConda
IsoPhase - Isoform-Level Phasing
Single-Cell RNA Sequencing using the Iso-Seq Method
Tutorial
Richard Kuo
Transcriptome Annotation by Modular Algorithms TAMA
TAMA (hands-on)
Tutorial
Conesa Lab
Installing tappAS
Quality Control and Characterization of LR Transcriptomes
SQANTI3 hands on and IsoAnnot
Hands-on tappAS
ETC
Closing thoughts
Workshop Photos
Github page
Biocore website
Pacific Biosciences website
Conesa lab website

Quick Introduction to the Workshop

The mission of the Bioinformatics Core facility is to facilitate outstanding omics-scale research through these activities:

welcome_figure1

Bioinformatics Core Staff and Students

Our team offers custom bioinformatics services to academic and private organizations. We have a strong academic background with a focus on cutting edge, open source software. We replicate standard analysis pipelines (best practices) when appropriate, and/or develop novel applications and pipelines when needed, however we always emphasize biological interpretation of the data.

staff

Collaboration with PacBio, Richard Kuo, and Conesa Lab

This workshop prominently features people from PacBio, the Roslin Institute, and Ana Conesa’s lab from the University of Florida. From PacBio Dr. Liz Tseng is a primary developer of much of (if not all of) PacBio’s Isoseq pipeline, Richard Kuo is a bioinformatician at the Roslin Institute and the creator and developer of the TAMA software package for transcriptome annotation of non-model organisms, and Dr. Ana Conesa and her lab are most notable for their software Blast2GO, maSigPro, Paintomics, NOISeq, SQANTI and tappAS, lab website (faculty page).

Ana Conesa
Conesa Lab

UCD Bioinformatics Core Contacts

Structure of the Virtual Workshops

Given the current Covid19 pandemic, and stay in place orders around the world, we’ve decided to take our popular bioinformatic workshops virtual. Our intent is to offer as close to an experience we can to our in-person workshops. We will hold the same goals and strive for a similar lecture/hand-on ratio. We will be using multiple technologies in order to help facilitate a maximum amount of interaction.

Zoom

Course lecture, discussions, and one-on-one help/troubleshooting will be conducted using a zoom meeting.

Because video is involved, we ask everyone to be respectful and we reserve the right to remove someone if they are being disrespectful or disruptive.

Learn more about how we use Zoom in our workshops.

Slack

Text based communication will be conducted via a Slack channel. Staff will be monitoring the Slack channel to answer questions (and schedule a Zoom break out room if needed). If you know the answer to someone else’s question, feel free to answer it.

Learn more about how we use Slack in our workshops.

Patience

We ask for a little more patience as this process is still new to us, but we are committed to providing you the best educational experience we can (under the current conditions).

Workshop Goals

Workshop Materials

Workshop materials are all posted on github, and publicly available

http://bioinformatics.ucdavis.edu/training

Computing Cluster

A portion of this course will be conducted on our servers and compute cluster (tadpole.genomecenter.ucdavis.edu).

Everyone should get an account.
https://computing.genomecenter.ucdavis.edu

Request an account -> sponsor is “Bioinformatics Core Workshop”

If you already have, or have had in the past, an account on our systems, then please tell us your username, or email, and we will add you to the workshop. Do not create a new account

Cluster usage will be under the slurm reservation ‘isoseq_workshop’