Route: rna-salmon

Transcript quantification of RNA-seq data using Salmon.

Segments:

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

Usage

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

cd <project dir>
git clone --depth 1 https://github.com/igordot/sns
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/*

Output

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.