RNA-seq Pipeline Overview
This section covers the analysis pipeline for RNA-seq data, used to quantify gene expression levels across the transcriptome.
What is RNA-seq?
RNA-seq (RNA sequencing) is a technique to study the transcriptome - measuring gene expression levels by sequencing RNA molecules.
Link to the RNA-seq pipeline:
Genomics_pipelines - RNAseq pipeline link
The README file in the repository provides detailed instructions on how to run the pipeline, including required software and dependencies.
Pipeline Steps
- Quality Control - FastQC analysis of raw reads
- Trimming - Removing adapters and low-quality bases (fastp)
- Alignment - Mapping reads to reference genome or transcriptome (STAR)
- Post-alignment processing - Filtering, duplicate removal, BAM file processing (samtools)
- Visualization - Creating bigWig files and plots (bamCoverage)
- Quantification - Counting reads per gene (featureCounts)
- Differential Expression Analysis - Statistical comparison between conditions (DESeq2)
Typical Outputs
- BAM files (aligned reads)
- BigWig files for visualization
- Count matrices (gene expression levels)
- QC reports