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. ├── 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 |
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Once the pipeline has finished running - Assess the results as follows:
NOTE: To proceed, you need to be on QUT’s WiFi network or signed via VPN.
To browse the working folder in the HPC type in the file finder:
Windows PC
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\\hpc-fs\work\training\ONTvariants |
Mac
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smb://hpc-fs/work/training/ONTvariants |
Once connected, browse to the “/ONTvariants/runs/run1_QC” folder.
Let’s open the “SRR17138639_QC_NanoPlot-report.html“ report:
Summary statistics
Metrics | dataset |
|---|---|
number_of_reads | 5513156 |
number_of_bases | 7815960904.0 |
median_read_length | 586.0 |
mean_read_length | 1417.7 |
read_length_stdev | 2997.2 |
n50 | 4054.0 |
mean_qual | 11.4 |
median_qual | 13.4 |
longest_read_(with_Q):1 | 199230 (3.7) |
longest_read_(with_Q):2 | 169532 (3.9) |
longest_read_(with_Q):3 | 134047 (3.6) |
longest_read_(with_Q):4 | 133337 (3.6) |
longest_read_(with_Q):5 | 115232 (3.3) |
highest_Q_read_(with_length):1 | 26.1 (290) |
highest_Q_read_(with_length):2 | 25.4 (202) |
highest_Q_read_(with_length):3 | 24.9 (331) |
highest_Q_read_(with_length):4 | 24.5 (232) |
highest_Q_read_(with_length):5 | 24.5 (243) |
Reads >Q5: | 5417207 (98.3%) 7502.8Mb |
Reads >Q7: | 5275906 (95.7%) 6978.9Mb |
Reads >Q10: | 4853447 (88.0%) 6056.6Mb |
Reads >Q12: | 3905370 (70.8%) 4809.9Mb |
Reads >Q15: | 1324999 (24.0%) 1571.9Mb |
Let’s first inspect the “SRR17138639_QC_LengthvsQualityScatterPlot_dot.png“ file. Alternatively for high resolution image open instead “SRR17138639_QC_LengthvsQualityScatterPlot_dot.html“
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