Quantification with Salmon

Salmon performs fast, accurate transcript quantification using quasi-mapping. NotchBio runs Salmon automatically on your preprocessed reads.

Running Salmon

1. Complete the preprocessing step first
2. Navigate to the Quantification step
3. Select the fastp version to use as input
4. Click Run

What Salmon Does

1. Maps preprocessed reads to the reference transcriptome
2. Quantifies transcript-level abundance
3. Produces per-gene counts for downstream analysis

Key Output Metrics

• Reads processed — Total reads mapped
• Mapping rate — Percentage of reads that mapped to the transcriptome
• Genes detected — Number of genes with non-zero counts

Interpreting Results

• Good mapping rate: > 70% for most organisms
• Low mapping rate may indicate contamination, wrong reference, or poor sample quality
• Genes detected typically ranges from 15,000–25,000 for human RNA-seq