.. _backbone-label:

Mirdeep2
==============================

Introduction
~~~~~~~~
miRDeep2 discovers active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, ...).


| For more information, please check:
| BioContainers: https://biocontainers.pro/tools/mirdeep2 
| Home page: https://github.com/rajewsky-lab/mirdeep2

.. note::
    Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions
~~~~~~~
.. list-table::
  :width: 100 %
  :widths: 25 75
  :header-rows: 1

  * - Cluster
    - Version(s)

  * - ANVIL
    - 2.0.1.3
  * - BELL
    - 2.0.1.3
  * - GAUTSCHI
    - 2.0.1.3
  * - NEGISHI
    - 2.0.1.3
  * - SCHOLAR
    - 2.0.1.3

Commands
~~~~~~~
- bwa_sam_converter.pl
- clip_adapters.pl
- collapse_reads_md.pl
- convert_bowtie_output.pl
- excise_precursors_iterative_final.pl
- excise_precursors.pl
- extract_miRNAs.pl
- fastaparse.pl
- fastaselect.pl
- fastq2fasta.pl
- find_read_count.pl
- geo2fasta.pl
- get_mirdeep2_precursors.pl
- illumina_to_fasta.pl
- make_html2.pl
- make_html.pl
- mapper.pl
- mirdeep2bed.pl
- miRDeep2_core_algorithm.pl
- miRDeep2.pl
- parse_mappings.pl
- perform_controls.pl
- permute_structure.pl
- prepare_signature.pl
- quantifier.pl
- remove_white_space_in_id.pl
- rna2dna.pl
- samFLAGinfo.pl
- sam_reads_collapse.pl
- sanity_check_genome.pl
- sanity_check_mapping_file.pl
- sanity_check_mature_ref.pl
- sanity_check_reads_ready_file.pl
- select_for_randfold.pl
- survey.pl

Module
~~~~~~~~
You can load the modules by::

    module load biocontainers
    module load mirdeep2

Example job
~~~~~
.. warning::
    Using ``#!/bin/sh -l`` as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use ``#!/bin/bash`` instead.

To run mirdeep2 on our clusters:

.. tab-set::

  .. tab-item:: Anvil

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A myallocation     # Allocation name
        #SBATCH -p wholenode        # Partition name
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=mirdeep2
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers mirdeep2

        # Your mirdeep2 workflow...

  .. tab-item:: Bell, Gautschi, or Negishi

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A mygroup     # Group name
        #SBATCH -p cpu         # Partition name
        #SBATCH -q normal      # QOS name (optional)
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=mirdeep2
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers mirdeep2

        # Your mirdeep2 workflow...

  .. tab-item:: Gautschi-AI

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A mygroup     # Group name
        #SBATCH -p ai          # Partition name
        #SBATCH --gres=gpu:1   # Number of GPUs
        #SBATCH -q normal      # QOS name (optional)
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=mirdeep2
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers mirdeep2

        # Your mirdeep2 workflow...

  .. tab-item:: Gilbreth

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A mygroup     # Group name
        #SBATCH -p a100        # Partition name
        #SBATCH --gres=gpu:1   # Number of GPUs
        #SBATCH --mem=2G       # Memory
        #SBATCH -q normal      # QOS name (optional)
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=mirdeep2
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers mirdeep2

        # Your mirdeep2 workflow...

  .. tab-item:: Scholar

    .. code-block:: bash

        #!/bin/bash
        #SBATCH -A queue     # Queue name
        #SBATCH -t 1:00:00
        #SBATCH -N 1
        #SBATCH -n 1
        #SBATCH --job-name=mirdeep2
        #SBATCH --mail-type=FAIL,BEGIN,END
        #SBATCH --error=%x-%J-%u.err
        #SBATCH --output=%x-%J-%u.out

        module --force purge
        module biocontainers mirdeep2

        # Your mirdeep2 workflow...