Day 3 - ryandkuster/EPP_575_RNA_25 GitHub Wiki

Agenda

Day 3 recording

Time	Lecture	Lab	Instructor
9:00	catch up
9:10	Introduce dataset		Ryan
9:20		Lab 01: Tour of ISAAC NG	Ryan
9:30	Library prep and trimming		Holly
9:40
9:50		Lab 02: QC	Allyson
10:00
10:10	10 minute break	:coffee:
10:20	Mapping With STAR		Ryan
10:30
10:40		Lab 03: Mapping with STAR	Allyson
10:50
11:00		Lab 04: IGV	Ryan
11:10
11:20

Day 3 Assignment:

Send the following to [email protected] by the end of the day.

1. Please send confirmation that you were able to successfully run fastqc (a screenshot of the output is fine).
2. Investigate the IGV read alignments. What is a splice junction and what do they look like in the aligned reads?
3. Investigate the IGV coverage track across several genes (in the gff track). What trend in coverage do you see at the beggining, middle, and end of the gene's exons?

RNA-Seq benchmarking and best practices

Links to articles and resources for RNA-Seq experimental design:

• A survey of best practices for RNA-seq data analysis
• RNA-seq differential expression studies: more sequence or more replication?
• Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size
• ENCODE best practices