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      Bulk RNA-Seq Analysis

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Discussion and Lectures
Intro to the Workshop
Schedule
What is Bioinformatics/Genomics?
Experimental Design and Cost Estimation
Closing thoughts
Data Reduction
Files and Filetypes
Prepare dataset
Preprocessing raw data
Indexing a Genome
Alignment with Star
Generating counts tables
Data analysis
Annotation from BioMart
Prepare R for data analysis
Differential Expression Analysis
Pathway Analysis
Prerequisites
CLI
R
Support
Cheat Sheets
Software and Links
Scripts
ETC
CAT website
Github page
Report Errors

Software and Links

Linux Terminal:

  1. Shell for Windows 10 tutorial
  2. Enable SSH tutorial OR
  3. MobaXterm
  4. PuTTY

R and RStudio

  1. R project
  2. RStudio Desktop
    Also see this link if you have trouble installing under Ubuntu

Software

  1. HTStream
  2. Star
  3. IGV
  4. MultiQC