Mirtop

Introduction

Mirtop is a ommand line tool to annotate with a standard naming miRNAs e isomiRs.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/mirtop

Home page: https://github.com/miRTop/mirtop

Versions

• 0.4.25

Commands

• mirtop

Module

You can load the modules by:

module load biocontainers
module load mirtop

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 mirtop on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=mirtop
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers mirtop

mirtop gff --format prost --sps hsa
    --hairpin examples/annotate/hairpin.fa \
    --gtf examples/annotate/hsa.gff3 \
    -o test_out \
    examples/prost/prost.example.txt