README.md

Group-5-miniproject_RNASEQ

As part of the EANBIT Virtual Residential Training 2020, this group will be working on a mini-project towards developing a snakemake workflow for RNA-Seq data processing and gene expression analysis. The detailed documentation is provided here

Group Members

1. Ruth Nanjala (Group Lead)
2. Kakembo Fredrick Elishama
3. Eric G. Kairuki
4. Stella E. Nabirye
5. Senamile Fezile Dlamini
6. Mthande S. Mzwakhile
7. Monica Mbabazi
8. Ritah Nabunje

A summary of the steps followed in our analysis include;

• Pre-processing of the reads
  • Quality Check using Fastqc and multiqc
  • Trimming of poor quality bases and filtering short reads using Trim_galore
  • Quality check using multiqc
• Alignment of samples to the reference. Two approaches were used;
  • Classical alignment using Hisat2
    • Count generation using Subreads feature count -Quality check using multiqc
  • Pseudo-alignment using Kallisto
• Differential Expression Analysis in R using DeSEq
• Converting the pipeline to R Markdown and Snakemake

A summary report of the workflow is documented on the Wiki page with the following sections;

1. RNA Seq Workflow
2. RNA Seq Workflow_Introduction
3. RNA Seq Workflow_Bash Script
4. RNA Seq Workflow_R Markdown Script.

• Link to the output report is here

5. RNA Seq Workflow_Snakemake
6. RNA Seq workflow_Challenges and Lessons