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Connecting to the HPC with PuTTY - QUT MediaHub
BYO data or download public small RNA-seq datasets
Either bring your own dataset or use the following guide to Download public small RNA-see data
Download Reference microRNA sequences from miRBase
Fetch First, let’s download a copy of miRBAse reference sequences, including hairpin and mature microRNA sequences.
microRNA mature sequences:
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wget https://www.mirbase.org/download/CURRENT/hairpin.fa gzip -c hairpin.fa > hairpin.fa.gz |
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wget https://www.mirbase.org/download/CURRENT/mature.fa gzip -c mature.fa.gz |
Alternatively, submit the following PBS Pro script to the cluster. Before running the script, create a ‘reference’ folder (i.e., /myteam/data/reference/ ).
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#!/bin/bash -l
#PBS -N nfsmrnaseq
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=24:00:00
cd $PBS_O_WORKDIR
wget https://www.mirbase.org/download/CURRENT/hairpin.fa
gzip -c hairpin.fa > hairpin.fa.gz
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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To submit the above command to the HPC cluster, prepare the following script:
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qjobs |
to check on the jobs, job that you are running. Note, Nextflow will launch additional jobs during the run.
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