Create working folder and copy data
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Let’s activate the conda environment:
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conda activate ONTvariantONTvariants_QC |
Next, we need to install few tools for today’s exercises. Now let’s go the https://anaconda.org and search for the following tools and instructions on how to install them:
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Alternative approach to create a conda env and install tools (we are not doing this - this just for your information) - installing all tools at once (slower option!)
Prepare the following environment.yml file:
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name: ONTvariants_QC channels: - conda-forge - defaults - bioconda dependencies: - nanoplot=1.42.0 - porechop=0.2.4 - porechop_abi=0.5.0 - chopper=0.8.0 |
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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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