Page Comparison

Pre-requisites:

• Review this one-hour-long detailed introduction to VIM editor: https://www.youtube.com/watch?v=IiwGbcd8S7I

• (optional) Familiarity with one unix text editors (for example Vi/Vim or Nano):

  • VIM ( https://bioinformatics.uconn.edu/vim-guide/ ; https://missing.csail.mit.edu/2020/editors/)

  • Nano (https://engineering.purdue.edu/ECN/Support/KB/Docs/BasictutorialforNanou ; https://www.howtogeek.com/howto/42980/the-beginners-guide-to-nano-the-linux-command-line-text-editor/ )

Installing Putty and connecting to the HPC (Windows users; Mac users can directly use the available ‘terminal’ app)

Install Putty:

Installing PuTTY - QUT Media Hub

...

Connecting to the HPC with PuTTY - QUT MediaHub

Download Reference microRNA sequences from miRBase

Fetch a copy of microRNA mature sequences:

...

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:

...

#!/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.

...

qsub launch.pbs

Monitoring the Run

You can use the command

qstat -u $USER

...

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

...

Copy and paste the path to the above script using VI or VIM (check prerequisites above).

Run the nextflow nf-core/smRNAseq pipeline.

Create a launch_nfsmRNAseq.pbs file that has the following information:

...