Project Description

This project is an investigation into Concordance of microarray and RNA-Seq differential gene expression.

Contributors

Luke Zhang Sri Veerisetti Benyu Zhou Mano Ranaweera

Repository Contents

This repository contains the scripts used for DESeq2 anlysis on RNA-seq differential expression data, Limma analysis on Microarray Differential Expression data as well as corcordance between microarray and RNA-Seq.

Order of Files

Below is the order in which the files should be run for the analysis pipeline and a description of each file:

1. STAR.qsub: Aligns spliced alignment of RNA-Seq data against the Rat Genome.
2. MultiQC.qsub: Gathers reports from various bioinformatics tools into one report, used for quality control purposes.
3. featurecounts.qsub: Counts the number of reads for a gene aligned to the reference
4. filteringProgrammer.R: Merge seperate count files and add control samples
5. deSeqProgrammer.R: Runs DeSeq2
6. analyst.R: Runs Limma
7. Project3_heatmap.R: Generates Clustered Heatmap
8. Pathway_Compare.ipynb: Performs enriched pathway comparisons