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

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:

#!/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...

#!/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...

#!/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...

#!/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...

#!/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...