Route: rna-salmon

Transcript quantification of RNA-seq data using Salmon.


  • Trim adapters and low quality bases (Trimmomatic).
  • Quantify (Salmon).
  • Summarize estimates for and gene-level analysis (tximport).


Set up a new analysis (common across all routes).

cd <project dir>
git clone --depth 1
sns/generate-settings <genome>
sns/gather-fastqs <fastq dir>

Run rna-salmon route.

sns/run rna-salmon

Check for potential problems.

grep "ERROR:" logs-sbatch/*


Primary results:

  • quant.salmon.tximport.counts.txt: Matrix of estimated counts for all genes and samples.
  • quant.salmon.tximport.counts.txt: Matrix of TPMs for all genes and samples.

Run metrics:

  • summary-combined.rna-salmon.csv: Summary table that includes the number of reads, the mapping rate, and the number of detected genes.