Description
Salmon is a tool for rapid transcript quantification from RNA-seq data. A set of target transcripts (either from a reference or de-novo assembly) is required for quantification. All you need to run Salmon is a FASTA file containing your reference transcripts and a (set of) FASTA/FASTQ file(s) containing your reads. Optionally, Salmon can use precomputed alignments (in SAM/BAM file format) of transcripts instead of raw reads.
Salmon's mapping-based mode takes place in two phases; indexing and quantification. The indexing step is independent of reads and needs to be run only once for a given set of reference transcripts. The quantification step is obviously specific to a set of RNA-seq reads and is therefore performed more frequently.
Versions
| Version | Module |
|---|---|
| 1.10.0 | scientific/salmon/1.10.0 |
Official documentation
https://salmon.readthedocs.io/en/latest/index.html
Primjer: https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/
Example
#PBS -N index
#PBS -q cpu
#PBS -l select=1:ncpus=20
cd ${PBS_O_WORKDIR}
module load scientific/salmon/1.10.0
salmon index -t gentrome.fa.gz -d decoys.txt -p $NCPUS -i salmon_index --gencode