Create working folder and copy data
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mkdir -p $HOME/workshop/ONTvariants mkdir -p $HOME/workshop/ONTvariants/data mkdir -p $HOME/workshop/ONTvariants/scripts mkdir -p $HOME/workshop/ONTvariants/runs/run1_QC mkdir -p $HOME/workshop/ONTvariants/runs/run2_mapping mkdir -p $HOME/workshop/ONTvariants/runs/run3_variant_calling |
Now, let let’s copy the scripts and data for today’s session:
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As outputs find the porechop_abi processed file (SRR17138639_1_porechop_abi.fastq) and the chopper output (SRR17138639_1_porechop_abi_chopper_q10_300b.fastq). To visualise the QC reports, let’s connect to the HPC via file finder (see below).
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:
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