Polyploidy Summer School: Homoeologous Expression Analysis

17 Jul. 2023

Moeko Okada

• https://github.com/MoekoOkada/SummerSchool_2023

How to setup the RENKU platform

• https://github.com/MoekoOkada/SummerSchool_2023/blob/main/Slides/RenkuSetup.qmd

Today's Plan

Slides: https://github.com/MoekoOkada/SummerSchool_2023/blob/main/Slides/HomoeologousExpressionAnalysis.qmd

Command lists

Part 1: https://github.com/MoekoOkada/SummerSchool_2023/blob/main/scripts/CommandLists1.md

1. Data download
2. Quality control
3. Homoeologous Mapping
4. Read sorting by EAGLE-RC
5. Read count
   1. read count
   2. make count matrix

Part 2: https://github.com/MoekoOkada/SummerSchool_2023/blob/main/scripts/CommandLists2.md

6. Expression analysis
   1. Clustering
   2. Homoeolog ratio test
   3. GO enrichment analysis (if we have time...)