Project overview
My first group project at Northeastern University for the course Introduction to Computational Methods in Bioinformatics (BINF6310) under Dr. Nabil Atallah. The project was a reproducibility study, where we worked on RNA-seq data of canine STS to distinguish between three subtypes of STS. We followed a specific pipeline and employed SLURM scripts, conda environment, and bioinformatics tools such as fastq-dump, fastQC, Bedtools, STAR, HTseq on Northeastern’s HPC cluster- Discovery. We utilized R packages such as DESeq2 and edgeR for differential expression analysis, PCA plot and heatmap generation.
