Page Comparison

...

Case 2: Run RNA-seq QC check

Preparing a ‘samplesheet.csv’ file

Prepare a sample sheet file that specifies the input files to be used. To do this, we use an nf-core script to generate the ‘samplesheet.csv’ file as follows (setting strandedness to auto allows the pipeline to determine the strandedness of your RNA-seq data automatically):

...

Case 3: Run RNA-seq pipeline

Adjusting the Trim Galore options

When the initial trimming is done, verify if any more clipping needs to be done and run the nf-core/rnaseq pipeline that will perform all the steps. For example:

#!/bin/bash -l
#PBS -N nfRNAseq
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=48:00:00

cd $PBS_O_WORKDIR
module load java
NXF_OPTS='-Xms1g -Xmx4g'

nextflow run nf-core/rnaseq --input samplesheet.csv \
        --outdir results \
        -r 3.12.0 \
        --genome GRCh38 \
        -profile singularity \
        --aligner star_salmon \
        --extra_trimgalore_args "--clip_r1 10 --clip_r2 10 --three_prime_clip_r1 1 --three_prime_clip_r2 1 "

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

...