mirdeep2.rst

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