This website contains materials for the Data Carpentry Genomics Workshop at University of Nevada, Reno two-day course (9:00 am-5:00pm), held on 15-16th January, 2019 at the Mathewson-IGT Knowledge Center - 107.
We are very excited to have you here and hope that we can get through a lot of material by the end of the workshop.
This workshop runs under a Code of Conduct. Please respect it and be excellent to each other!
Twitter hash tag: #DCUNR
Notes from the course:
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 Elias and Sateesh assist with in their capacity as certified Carpentry Instructors.
Day-1
09:00-09:45am Introduction and Genomics Workshop Overview
09:45-10:30am Introduction to CyVerse Atmosphere Cloud
10:30-10:45am Coffee/Tea break
10:45-12:00pm BASH- Command Line for Genomics
12:00-1:30pm Lunch Break (lunch will be provided!)
01:30-2:45pm BASH - continued & Bioconda
02:45-3:00pm Coffee/Tea Break
03:00-4:00pm RNAseq overview and Trimming sequencing data
04:00-5:00pm Version control with Github
Day-2
09:00-10:30am Transcriptome Assembly
10:30-10:45am Coffee/Tea Break
10:45-12:00pm Read Quantification
12:00-1:30pm Lunch Break (lunch will be provided!)
01:30-2:30pm Differential Expression
02:30-2:45pm Coffee/Tea Break
02:45-5:00pm Project Organization and Markdown