Create working folder and copy data
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Create a conda environment called ONTvariants_nanoplotQC
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conda create -n ONTvariants_QC |
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Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/barrero/miniconda3/envs/ONTvariants_nanoplotQC Proceed ([y]/n)? y Preparing transaction: done Verifying transaction: done Executing transaction: done # # To activate this environment, use # # $ conda activate ONTvariants_nanoplotQC # # To deactivate an active environment, use # # $ conda deactivate |
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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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