Salmon

De acordo com o página do Salmon, “Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It requires a set of target transcripts (either from a reference or de-novo assembly) to quantify. 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 make use of pre-computed alignments (in the form of a SAM/BAM file) to the transcripts rather than the raw reads. The mapping-based mode of Salmon runs in two phases; indexing and quantification. The indexing step is independent of the reads, and only need to be run one for a particular set of reference transcripts. The quantification step, obviously, is specific to the set of RNA-seq reads and is thus run more frequently”.

Versões Disponíveis

• salmon/0.14.0

Submissão de Jobs

Crie um arquivo chamado, por exemplo, submit_jobs.sh.

#!/bin/bash
#SBATCH -t 20:00:00

module load salmon/0.14.0

export INPUT="transcripts.fasta reads_1.fastq reads_2.fastq run.sh"
export OUTPUT="transcripts_index transcripts_quant"

job-nanny ./run.sh

em que o script run.sh tem o seguinte conteúdo:

#!/bin/bash

echo ""
echo "===========[[ Preparing transcriptome indices ]]========================="
echo ""
salmon index -t transcripts.fasta -i transcripts_index -k 31

echo ""
echo "===========[[ Quantifying in mapping-based mode - 1 ]]==================="
echo ""
salmon quant -i transcripts_index -l A -1 reads_1.fastq -2 reads_2.fastq --validateMappings -o transcripts_quant

echo ""
echo "===========[[ Quantifying in mapping-based mode - 2 ]]==================="
echo ""
salmon quant -i transcripts_index -l A -r reads_1.fastq --validateMappings -o transcripts_quant

Antes de submeter o job, deve-se tornar o script executável pelo comando

chmod +x run.sh

Para submeter o processo, basta usar o comando:

sbatch submit_jobs.sh

Referências

Para informações adicionais sobre o software, consulte a documentação do Salmon.