Mirdeep2#

Introduction#

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

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

Example job#

Adjust slurm options based on job requirements (slurm cheat sheet):

#!/bin/bash
#SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
#SBATCH -N 1   # Number of nodes
#SBATCH -n 1   # Number of tasks per node
#SBATCH -c 4   # Number of CPU cores per task
#SBATCH --mem=8G       # Memory required per node
#SBATCH --job-name=mirdeep2    # Job name
#SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
#SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
#SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
#SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

module purge   ### Optional, but highly recommended.
module load mirdeep2/XXXX      ### Latest version is recommended.