1. Welcome to SETAC-NA 2018 RNAseq workshop!

This website contains materials for the mRNAseq Data Workshop: De Novo Assembly and Differential Expression Analysis full-day course (8:00 am-5:00pm), held on 4 November, 2018 at the SETAC North America meeting, at the Sacramento Convention Center in room CC-311.

We are very excited to have you here and hope that we can get through a lot of material today!

This workshop runs under a Code of Conduct. Please respect it and be excellent to each other!

Twitter hash tag: #SETACSacramento

Notes from the course:

Hackmd.io

1.1. Instructors

• Lisa Johnson
• Jane Park
• Elias Oziolor

This workshop incorporates materials from the Analysis of Next Generation Sequencing or ANGUS and several nonmodel RNAseq workshops. We recommend you visit and explore these materials! ANGUS materials are taught at the Data Intensive Biology Summer Institute or DIBSI coordinated at UC Davis every summer by Dr. Titus Brown, which Lisa, Jane and Elias assist with in their capacity as certified Carpentry Instructors.

1.2. Schedule in brief

• 8:00-9:00am Introduction and RNASeq overview
• 9:00-10:00am Jetstream lesson
  • logging in with a private key
  • working with bioconda
• 10:00-10:15am Coffee and sugar
• 10:15-11:00am Bash
• 11:00am-12:00pm Trimming sequencing data
• 12:00-1:30pm Lunch
• 1:30-2:45pm Transcriptome assembly
• 2:45-3:00pm Coffee and sugar
• 3:00-4:00pm Read quantification
• 4:00-5:00pm Differential expression

1.3. Other info

• These lessons are based on the original Eel Pond Protocol, then edited in 2016 and automated by Dr. Tessa Pierce.
• Two other nonmodel RNAseq workshops: DIBSI 2017 and SIO-BUG 2017
• Install software on your own systems: here are instructions for downloading and installing the software on the ‘RNASeq_1DayWorkshop’ Jetstream image,
• Backup files, if something goes wrong
• If you find that you would like more practice working on the command line, here is a command-line bootcamp. In addition, BASH training videos are freely available through the NH-INBRE program, the UNH Bioinformatics Core facility.
• Source documents for these lessons can be found on GitHub.