Day 5 - ryandkuster/EPP_575_RNA_25 GitHub Wiki

Agenda

Time	Lecture	Lab	Instructor
9:00	ISAAC-NG		Izaak
9:10
9:20		Lab 06: DESeq2	Ryan
9:30
9:40
10:00
10:10	10 minute break	:coffee:
10:20	scRNA-Seq		Trevor
10:30
10:40
10:50	Gene Ontology	Lab 07: GO lab	Ryan
11:00
11:10
11:20

Day 5 Assignment:

Send the following to [email protected] by the end of the day. If you have encountered any issues with accessing materials or command line functionality, please also indicate this in the email.

Previously, we created a results object and MA plot with a contrast (0h vs. 3h) and an adjusted p-value cutoff (FDR) of 0.05:

res <- results(dds, alpha = 0.05, contrast = c("hours_cold", "0h", "3h"))
plotMA(res, ylim=c(-10, 10))

Send a screenshot or saved image of the original MA plot, then, adjust the alpha value to be much higher or lower and send a screenshot of the new MA plot. What changed between the two plots?

Writing Assignment

Finally, don't forget that the Journal Article Writing Assignment is due one week from today on June 18th. Please feel free to turn this in earlier.

Each student will select a peer-reviewed journal article about RNA-Seq analysis relevant to their field of research and write a two page summary and critical review of the experimental design and analysis methods, due the following Tuesday, June 18th. Email to [email protected].

The document should cover the following topics:

Brief summary of the study's hypothesis. (8 points)
Why was RNA-Seq selected as an experimental method? (ie how does it relate to the biology of the hypothesis?) (8 points)
Is the technology selected appropriate for addressing the hypothesis? (8 points)
What is the experimental design? What were the technical/biological replicates, if present? What software was used? (8 points)
What do you think are the strengths or weaknesses of the paper? (8 points)

UTK Bioinformatics Resources and HPSC links

OIT HPSC homepage
https://oit.utk.edu/hpsc

Bioinformatics Computing Support | OIT HPSC
https://tiny.utk.edu/BCS

Fundamentals of HPC for Bioinformatics workshop series
https://tiny.utk.edu/HPC-Bioinformatics

Getting Help
Call the OIT Help Desk at (865) 974-9900

From the OIT HPSC homepage (https://oit.utk.edu/hpsc):
Submit a service request

Office hours
OIT HPSC Workshop Recordings: https://oit.utk.edu/hpsc/overview/workshop-recordings/

Single cell resources

Single-cell best practices – https://www.sc-best-practices.org/preamble.html
Best practices for single-cell analysis across modalities — A review by the authors of guide above. https://doi.org/10.1038/s41576-023-00586-w

scverse tutorials – https://scverse.org/learn/