Group-5-miniproject_RNASEQ

As part of the EANBIT Virtual Residential Training 2020, this group will be working on a mini-project towards an RNA-Seq data processing and gene expression analysis workflow.

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