Quality Control, Mapping and Reads Count for RNA-Seq Analysis

RNA-seq workflow for UALBANY CFG - Demux, QC, Vis, Align, preProcess, DGE Calls

An R package to parse and manage text output of the sequencing quality control utility (fastQC)

Walks through installation and usage of FASTQC, MultiQC, Trimmomatic, and Salmon for transcriptomic data preprocessing. Includes Grid Engine shell scripts that can be looped over many files in a directory.

A reproducible RNA-Seq analysis pipeline for Staphylococcus aureus under antibiotic stress, utilizing Nextflow and Singularity. It involves genome mapping, read counting, and statistical analysis to identify differentially expressed genes (DEGs) and generates key visualizations.