Week 4: RNAseq
Section Links
Week 4 Overview
For the final week, use this time to finish up any tasks you weren’t able to complete. There are no nextflow tasks this week, but you will be asked to create some figures from the original paper using your own findings.
Objectives
Read the original publication with a specific focus on their RNAseq experiment
Reproduce figures 3C and 3F with your own findings and compare them in your discussion
Write a short methods section for your pipeline and compare with the methods published in the original paper
Read the original paper
The original publication was given to you in a post on blackboard. Please read the paper and focus specifically on their analysis and discussion of their RNAseq experiment.
Replicate figure 3C and 3F
Focus on figure 3C and specifically their discussion of their RNAseq results.
Create a volcano plot similar to the one seen in figure 3c. Use your DAVID or GSEA results and create a plot with the same information as 3F using your findings.
Read their discussion of their results and specifically address the following in your provided notebook:
Compare how many significant genes are up- and down-regulated in their findings and yours (using their significance threshold). Ensure you list how many you find vs. how many they report.
Compare their enrichment results with your DAVID and GSEA analysis. Comment on any differences you observe and why there are discrepancies.
Write a methods section for your pipeline
We will have briefly discussed how to write a methods section. Please write a methods section for the workflow you’ve implemented with your pipeline in the style we’ve discussed.
In your provided notebook, write a brief methods section for your workflow
Read the methods for the paper and in your provided notebook, please ensure you briefly discuss any differences in the methods you used and how that may change what results you find.