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Download Reference microRNA sequences from miRBase
Fetch a copy of microRNA mature sequences:
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wget https://www.mirbase.org/download/CURRENT/mature.fa gzip -c mature.fa.gz |
Run a test
Before running the pipeline with real data, run the following test:
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#!/bin/bash -l #PBS -N nfsmrnaseq #PBS -l select=1:ncpus=2:mem=4gb #PBS -l walltime=24:00:00 #work on current directory (folder) cd $PBS_O_WORKDIR #load java and set up memory settings to run nextflow module load java NXF_OPTS='-Xms1g -Xmx4g' nextflow run nf-core/smrnaseq -profile test,singularity --outdir results -r 2.1.0 |
Submitting the job
Once you have created the folder for the run, the samplesheet.csv file, nextflow.config, and launch.pbs, you are ready to submit.
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qsub launch.pbs |
Monitoring the Run
You can use the command
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qstat -u $USER |
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You can also check the .nextflow.log file for details on what is going on.
Preparing a sample metadata file
Now let’s prepare a samplesheet.csv file that specifies the name of your samples and the location of the raw FASTQ files
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