miRDeep2

Introduction

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

For more information, please check its website: https://biocontainers.pro/tools/mirdeep2 and its home page on Github.

Versions

  • 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 -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
ml biocontainers mirdeep2