Day 4 - ryandkuster/EPP_575_RNA_25 GitHub Wiki
Agenda
| Time | Lecture | Lab | Instructor |
|---|---|---|---|
| 9:00 | IGV catch-up | ||
| 9:10 | Counting (HTSeq and featureCounts) | Ryan | |
| 9:20 | Pseudoalignment with Salmon | Ryan | |
| 9:30 | Lab 05: Read Counting | Ryan | |
| 9:40 | |||
| 9:50 | Count normalization and analysis | Ryan | |
| 10:00 | |||
| 10:10 | 10 minute break | :coffee: | |
| 10:20 | |||
| 10:30 | |||
| 10:40 | Lab 06: set up RStudio and packages | Allyson | |
| 10:50 | |||
| 11:00 | Lab 06: DESeq2 | ||
| 11:10 | |||
| 11:20 |
Day 4 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.
Pick any gene from Fig. 8D in the study from our dataset. Using either the desktop or web-based IGV, search for this gene name and capture a screenshot showing the gene's coverage for the two RNA-Seq alignments (Col_0h and Col_3h). Note: the name may need to be searched at https://www.arabidopsis.org if it is not found from IGV search.
In addition to the image, describe which sample appears to have higher coverage. Given the context of the normalization steps used by DESeq2, if two samples appear to have greatly different coverage for a single gene, this doesn't guarantee that the gene will be differentially expressed. Why not?