QuickMIRSeq
Introduction
QuickMIRSeq is an integrated pipeline for quick and accurate quantification of known miRNAs and isomiRs by jointly processing multiple samples.
Versions
1.0
Commands
perl
QuickMIRSeq-report.sh
Module
You can load the modules by:
module load biocontainers
module load quickmirseq
Note
This module defines program installation directory (note: inside the container!) as environment variable $QuickMIRSeq. Once again, this is not a host path, this path is only available from inside the container.
With the way this module is organized, you should be able to use the variable freely for both the perl $QuickMIRSeq/QuickMIRSeq.pl allIDs.txt run.config and the $QuickMIRSeq/QuickMIRSeq-report.sh steps as directed by the user guide.
A simple QuickMIRSeq.pl and QuickMIRSeq-report.sh will also work (and can be a backup if the variable expansion somehow does not work for you).
You will also need a run configuration file. You can copy from an existing one, or take from the user guide, or as a last resort, use Singularity to copy the template (in $QuickMIRSeq/run.config.template) from inside the container image. singularity shell may be an easiest way for the latter.
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 QuickMIRSeq on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=quickmirseq
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers quickmirseq
quickmerge -d out.rq.delta -q q.fasta -r scab8722.fasta -hco 5.0 -c 1.5 -l n -ml m -p prefix