Pipeline Overview

NotchBio provides a complete RNA-seq analysis pipeline that takes your raw FASTQ files through quality control, preprocessing, quantification, differential expression analysis, and gene set enrichment analysis.

Pipeline Steps

Step	Tool	Purpose
Quality Control	FastQC	Assess raw data quality
Preprocessing	fastp	Trim adapters and low-quality bases
Quantification	Salmon	Map reads and quantify transcripts
Differential Expression	DESeq2	Find differentially expressed genes
Gene Set Enrichment	GSEA	Identify enriched biological pathways

How It Works

1. Each step runs in the cloud on dedicated compute resources
2. Results are versioned — you can re-run steps with different parameters
3. Downstream steps automatically use upstream outputs
4. All runs are reproducible and shareable

Versioning

Every pipeline run creates a version that records:

• The parameters used
• Which samples were processed
• The input version (upstream step used)
• Status and results for each sample

Next Steps

• Quality Control — Understand your data quality
• Preprocessing — Clean up your reads
• Quantification — Map and count transcripts
• Differential Expression — Find significant genes
• GSEA — Explore biological pathways