...
Line 1: Defines that the script is a bash script.
Lines 2-5: Are commented out with “#” at the beginning and are ignored by bash, however, these PBS lines tell the scholar (PBS Pro) the name of the job (line 2), the number of CPUs and RAM memory to use (line 3), the time to run the script (line 4) and report if there are any errors (line 5).
Line 7: Tells the job to run on the current directory.
Line 9: Activate the conda environment where the QC tools were installed using conda.
Lines 11-17: User defined variables. Modify the FASTQ, genome and/or sample ID to use to run the job as appropriate. Note: in the lines below, the variable names are used instead of the actual names or locations of the files (e.g., $FASTQ)
Line 20: Run a Quality Control (QC) overview of the raw Nanopore reads using NanoPlot
Line 23: Remove adapter sequences from the 5'- and 3’-ends of the raw reads
Line 26: Filter reads with a quality score below Q10 (90% accuracy; -q 10) and shorter than 300 bases (-l 300)
Submit the QC job to the HPC cluster:
| Code Block |
|---|
qsub launch_ONTvariants_QC.pbs |
Monitor the progress of the job:
| Code Block |
|---|
qjobs |
The job will take ~30 - 40 min to complete.
Outputs
The following list of outputs will be generated once the job has completed:
| Code Block |
|---|
.
├── launch_ONTvariants_QC.pbs
├── SRR17138639_1_porechop_abi_chopper_q10_300b.fa
├── SRR17138639_1_porechop_abi_chopper_q10_300b.fa_stats.txt
├── SRR17138639_1_porechop_abi_chopper_q10_300b.fastq
├── SRR17138639_1_porechop_abi.fastq
├── SRR17138639.fastq.gz
├── SRR17138639_QC_LengthvsQualityScatterPlot_dot.html
├── SRR17138639_QC_LengthvsQualityScatterPlot_dot.png
├── SRR17138639_QC_NanoPlot_20240517_2037.log
├── SRR17138639_QC_NanoPlot-report.html
├── SRR17138639_QC_NanoStats.txt
├── SRR17138639_QC_Non_weightedHistogramReadlength.html
├── SRR17138639_QC_Non_weightedHistogramReadlength.png
├── SRR17138639_QC_Non_weightedLogTransformed_HistogramReadlength.html
├── SRR17138639_QC_Non_weightedLogTransformed_HistogramReadlength.png
├── SRR17138639_QC_WeightedHistogramReadlength.html
├── SRR17138639_QC_WeightedHistogramReadlength.png
├── SRR17138639_QC_WeightedLogTransformed_HistogramReadlength.html
├── SRR17138639_QC_WeightedLogTransformed_HistogramReadlength.png
├── SRR17138639_QC_Yield_By_Length.html
└── SRR17138639_QC_Yield_By_Length.png |
Let’s inspect the QC reports, for these you will need to connect to HPC via file finder as follows: