Bioinformatics Workshop: PacBio Full-Length RNA Kinnex

Basic Information:

Wednesday - Friday June 4-6, 2025, 10 a.m. - 2 p.m (Wed/Thurs, Remote) 10 a.m. - 2 p.m. (Friday, Remote/In-Person Mission Bay)

Organizer - UCSF CAT Bioinformatics

Contact - [email protected]

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

Cost - UC and Affiliate Rate: $600, Other Academic/Non-Profit: $900, For-Profit: $1200 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:

Unlock Full-Length Transcript Insights with Kinnex MAS-Seq and PacBio Long Reads

This workshop explores how Kinnex, leveraging the MAS-Seq method for high-throughput full-length cDNA concatenation, combined with PacBio Revio long-read sequencing, enables comprehensive transcript-level studies. Discover the power of the Iso-Seq method for whole transcriptome profiling, revealing critical differential transcript usage that can elucidate underlying pathology beyond standard gene-level analysis.

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

Bulk RNA Kinnex PacBio Workshop (3 Days)

Day 1-2: Processing bulk long-read data: command-line tools for software setup, pipeline creation, execution on a provided dataset to generate transcripts and counts. Day 2 includes in-depth isoform discovery and abundance estimation.

Day 3: Bulk RNA analysis in command line and R: transcript and gene-level analysis, workflow creation/modification, and data quality assessment. Includes discussions on experimental design, data generation, and analysis principles throughout.

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.

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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.

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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.

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