3 Quality Control

This report covers the quality control and exploratory analysis of bulk RNA-seq data from Escherichia coli* K-12 MG1655.

The list of contrasts of interest is:

• DE between [condition A] vs [condition B]
• DE between [condition C] vs [condition D]

Topics covered

• Exploratory data analyses
• Sanity Checks

Data

• Reference data used: E. coli* K-12 MG1655 NCBI RefSeq: NC_000913.3

• Input data is the output from the nf-core rnaseq pipeline salmon.merged.gene.SummarizedExperiment.rds

📘 Note: E. coli MG1655 is a prokaryote. Key differences to keep in mind:

• No introns → transcript = gene (tx2gene mapping is 1:1)
• Genome size ~4.6 Mb with ~4,300 genes
• Enrichment analysis via KEGG or custom gene sets with fgsea

Explanation of the QC analysis 🧾

This document guides you through the standard QC pipeline for prokaryotic bulk RNA-seq data processed with nf-core/rnaseq Bowtie2 + Salmon. It is structured to be both educational and reproducible.