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
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