Schedule

As the workshop progresses the schedule may be updated

Monday, July 27

8:50 am Zoom session starts
9:00 am Welcome, format and expectations and introductions
9:30 am Connections, logging in, environment
9:45 am Intro CLI/Adv CLI to Command Line
10:00 am Hands on
10:15 am 15 minute break
10:30 am Intro CLI/Adv CLI to Command Line
10:45 am Hands on
11:00 am Intro CLI/Adv CLI to Command Line
11:15 am Hands on
11:30 am Intro CLI/Adv CLI to Command Line
11:45 am Hands on
12:00 pm Lunch hour
1:00 pm Genomics/Bioinformatics Talk
2:00 pm Running jobs on a cluster
2:15 pm Hands on
2:30 pm Running jobs on a cluster
2:45 pm Hands on
3:00 pm 15 minute Break
3:15 pm Files and file types (fastq)
3:30 pm Dataset description and setup
3:45 pm Hands on
4:00 pm Dataset description and setup
4:15 pm Hands on
4:45 pm Recap and Homework
5:00 pm Zoom session ends

Tuesday, July 28

8:50 am Zoom session starts
9:00 am Recap and check everyones session
9:15 am Data checkin, preprocessing
9:30 am Hands on
9:45 am preprocessing
10:00 am Hands on
10:15 am 15 minute break
10:30 am preprocessing
10:45 am Hands on
11:00 pm preprocessing
11:15 pm Hands on
11:30 pm preprocessing
11:45 pm Hands on
12:00 pm Lunch hour
1:00 pm Technology Seminar by Lutz Froenicke
2:00 pm preprocessing
2:45 pm 15 minute break
2:30 pm Hands on
3:00 pm preprocessing QA/QC
3:30 pm Hands on
4:00 pm preprocessing Recap
4:30 pm Aligments References
3:30 pm Hands on
4:45 pm Recap and Homework and Extra
5:00 pm Zoom session ends

Wednesday, July 29

8:50 am Zoom session starts
9:00 am Recap and questions
9:10 am preprocessing QA/QC
9:20 am Files and file types (fasta/gtf)
9:30 am Aligments
10:00 am Hands on
10:30 am 15 minute break
10:45 am Aligments
11:15 am Hands on
11:45 am Aligments Recap
12:00 pm Lunch hour
1:00 pm Files and file types (sam/bam)
1:30 pm Creating counts tables
2:00 pm Hands on
2:30 pm 15 minute break
2:45 pm Alignment with Salmon
3:15 pm Hands on
4:45 pm Closing
5:00 pm Zoom session ends

Thursday, July 30

8:50 am Zoom session starts
9:00 am Recap and questions
9:15 am Intro/Adv R
9:30 am Hands on
9:45 am Intro/Adv R
10:00 am Hands on
10:15 am 15 minute break
10:30 am Intro/Adv R
11:00 am Hands on
11:45 am Prepare R for DE
12:00 pm Lunch hour
1:00 pm Experimental Design
2:00 pm Retreiving Annotation
2:20 pm Hands on
2:45 pm 15 minute break
3:00 pm Differential Expression Analysis
3:20 pm Hands on
3:40 pm Differential Expression Analysis
4:00 pm Hands on
4:20 pm Differential Expression Analysis
4:30 pm Hands on
4:45 pm Recap, Homework, and Extra
5:00 pm Zoom session ends

Friday, July 31

8:50 am Zoom session starts
9:00 am Recap and questions
9:30 am Differential Expression Analysis
10:00 am Hands on
10:30 am Differential Expression Analysis
11:00 am Hands on
11:15 am Differential Expression Analysis
11:40 am Hands on
12:00 pm Lunch hour
1:00 pm Differential Expression Analysis
1:30 pm Hands on
2:00 pm Functional Enrichment Analysis
2:30 pm Hands on
3:00 pm 15 minute break
3:15 pm Functional Enrichment Analysis
3:45 pm Hands on
4:15 pm Star vs Salmon
4:45 pm Closing
5:00 pm Zoom session ends