Bioinformatics Workshop: PacBio Full-Length RNA Kinnex

Basic Information:

Wednesday - Friday April 16-18, 2025, 9 a.m. - 5 p.m (Wed/Thurs, Remote) 10 a.m. - 4 p.m. (Friday, In-Person Mission Bay)

Organizer - UCSF CAT Bioinformatics

Contact - [email protected]

Location - Hybrid Wed/Thurs Remote and Friday In Person Genentech Hall, Teaching Lab Room 227

Cost - UC and Affiliate Rate: $1200, Other Academic/Non-Profit: $1500, For-Profit: $2000 all per person

via CAT iLabs submission under 'CAT Bioinformatics: Workshop', the Credit Card option is not available this time.

Seats Available - 25 Seats

Workshop Description:

PacBio Kinnex is based on the MAS-Seq method, which concatenates smaller fragments into larger fragment libraries in order to increase throughput. Kinnex Full-length RNA libraries sequenced on PacBio Revio long-read sequencing systems enable large-scale transcript-level studies at a resolution difficult to attain with short-read RNA sequencing. Using the Iso-Seq method for whole transcriptome profiling allows for differential transcript usage discovery that can explain underlying pathology, even in cases where gene-level differential expression is absent.

This is a Three-day hybrid remote/in-person workshop.

Day 1 - Day 2 will involve data reduction from raw data to transcripts and counts. The first day will primarily be on the command line and include software installation, creating a pipeline, and executing it on a provided dataset (a very small dataset) that can be completed within the time frame of the course and on a personal laptop.

Second Half of Day 2 will explore both Isoform discovery and abundance information

Day 3 will perform analysis both at the transcript and gene level using both the command line and R, create and modify workflows, and diagnose and treat problematic data.

Sprinkled within will be additional talks and conversations, including experimental design, data generation, and philosophy of analysis.

Prerequisites:

This course does not provide instruction in the basics of the command line or R for bioinformatics. To get the most out of the workshop an intermediate understanding of the command line and the R statistical programming language are necessary.

All work will be performed on each individual's laptop using a small data set created specifically for the course and to complete in the time alloted.

First Name *

Last Name *

Email Address *

Department(UCSF)/Institution/Company *

Principle Investigator/Group

sharemyinfo

Please do not share my registration information with any potential sponsors.

sunshine

I am a physician, and my interactions with vendors or sponsors may be subject to reporting under the Physician Payments Sunshine Act.

When are you generating Pac Bio Kinnex Full-Length RNA data? *

Cancellation Policy:

Registrants are requested to be cognizant that only so many seats for a workshop may be available and should notify the Core ([email protected]) as soon as they know they are unable to attend so that we can notify and accept someone on the waitlist that a spot has become available.

Referencing the CAT Core and Publications

When submitting manuscripts, please acknowledge the CAT by including the text: “Sequencing was performed at the UCSF CAT, supported by UCSF PBBR, RRP IMIA, and NIH 1S10OD028511-01 grants.”

To aid our facility in future grant submissions, it helps to reference labs and publications that have benefited from our core please notify us of your achievement by emailing catcore [at] ucsf.edu the PMID number, lab, and the piece of equipment used in the paper.