albert-ying/autonomous-lab/salmon

Salmon - RNA-Seq Transcript Quantification

When to Use

Use Salmon for fast, accurate transcript-level quantification from RNA-Seq reads. Salmon uses quasi-mapping to align reads directly to a transcriptome reference without requiring genome alignment.

Standard Workflow

1. Build Index

salmon index -t transcriptome.fa -i salmon_index

2. Quantify (paired-end)

salmon quant -i salmon_index -l A \
  -1 reads_1.fq.gz -2 reads_2.fq.gz \
  -o salmon_output \
  --validateMappings

• -l A auto-detects library type
• --validateMappings improves accuracy

3. Output

Results in salmon_output/quant.sf:

• Name: transcript ID
• NumReads: estimated read count
• TPM: transcripts per million
• Length, EffectiveLength: transcript lengths

Key Decisions

• For simulated data with exact counts, use NumReads column and round to integers
• Use --validateMappings for best accuracy
• For transcript-level quantification (not gene-level), no additional summarization needed

Installation

conda install -c bioconda salmon
# or
mamba install -c bioconda salmon