mirdeep2
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'mirdeep2' Versions
- 2.0.1.3
Link to section 'Commands' of 'mirdeep2' 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
Link to section 'Module' of 'mirdeep2' Module
You can load the modules by:
module load biocontainers
module load mirdeep2
Link to section 'Example job' of 'mirdeep2' Example job
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
miRDeep2.pl reads_collapsed.fa genome.fa reads_collapsed_vs_genome.arf \
miRBase_mmu_v14.fa miRBase_rno_v14.fa precursors_ref_this_species.fa \
-t Mouse 2>report.log