.. _Salmon:

Salmon
======

De acordo com o `página do Salmon <https://salmon.readthedocs.io/en/latest/salmon.html>`_,
"*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*.

.. code-block:: bash

  #!/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:

.. code-block:: bash

  #!/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

.. code-block:: bash

   chmod +x run.sh

Para submeter o processo, basta usar o comando:

.. code-block:: bash

  sbatch submit_jobs.sh

Referências
-----------

Para informações adicionais sobre o software, consulte a `documentação do Salmon <https://salmon.readthedocs.io/en/latest/index.html>`_.