Workshop Schedule

Day 1

Time	Topic	Instructor
9:00 - 9:40	Workshop Introduction	Meeta
9:40 - 10:30	Introduction to the Shell	Mary
10:30 - 10:45	Break
10:45 - 11:35	Introduction to the Shell (cont.)	Meeta
11:35 - 12:15	Searching and Redirection	Mary
12:15 - 13:15	Lunch
13:15 - 13:45	Introduction to the Vim Text Editor	Mary
13:45 - 15:00	Loops and Shell Scripts	Meeta
15:00 - 15:15	Break
15:15 - 15:45	Permissions and Environment Variables	Mary
15:45 - 17:00	Project Organization and Best Practices in Data Management	Meeta

Time	Topic	Instructor
9:00 - 9:45	Introduction to High-Performance Computing for HMS-RC’s O2	Meeta
9:45 - 10:00	Break
10:00 - 11:15	Introduction to RNA-seq and Library Prep	Mary
11:15 - 11:55	NGS workflows and data standards	Meeta
11:55 - 12:55	Lunch
12:55 - 13:50	Quality Assessment of Sequence Data	Mary
13:50 - 14:30	Sequence Alignment Theory	Meeta
14:30 - 14:45	Break
14:45 - 16:00	RNA-seq Alignment with STAR	Mary
16:00 - 17:00	Assessing Alignment Quality	Meeta

Time	Topic	Instructor
9:00 - 10:15	Generating a Count Matrix	Meeta
10:15 - 10:45	Documenting Steps in the Workflow with MultiQC	Meeta
10:45 - 11:00	Break
11:00 - 12:35	Automating the RNA-seq workflow	Mary
12:35 - 13:35	Lunch
13:35 - 13:45	Alternative workflows for analyzing RNA-seq data	Mary
13:45 - 15:20	Quantifying expression using alignment-free methods (Salmon)	Meeta
15:20 - 15:35	Break
15:35 - 15:45	Other Applications of RNA-seq	Mary
15:45 - 16:25	Troubleshooting RNA-seq Data Analysis	Mary
16:25 - 17:00	Genome Builds and Accessing Data on GEO/SRA	Meeta
	Wrap-up	Mary