README.md

BF528- FINAL PROJECT - SINGLE CELL AND BULK mRNA SEQUENCING

This repository contains the contents of the final project. All scripts and output files can be accessed through the /projectnb/bf528/students/rshreej/Project5-BF528/ on SCC.

The sections that are involved in the final project are:

I chose the following sections to try to work on single cell analysis and STAR alignment. The datasets are from Baron et al (Section 1 and 2) and Wang et al (Section 3)

Section 1: Project 4: Processing the UMI counts matrix (Programmer)

Section 2: Project 4: Cluster marker genes (Analyst)

Section 3: Project 3: RNA-Seq Sample Statistics and Alignment (Data- Curator)

REPOSITORY CONTENTS

Scripts/section 1 and 2.R - R script for section 1 and 2

Scripts/fastqc.qsub - script for section 3 fastqc

Scripts/multiqc.qsub - script for section 3 multiqc

Scripts/star.qsub - script for section 3 star

FINAL PROJECT.pdf - writeup

CONTRIBUTOR

ROJASHREE JAYAKUMAR