Create working folder and copy data
...
Create a conda environments
Approach 1: install tools one at a time
Create a conda environment called ONTvariants_QC
...
| Code Block |
|---|
conda install bioconda::seqkit |
...
Approach 2: Create environment and install tools
...
all
...
at once
...
This is a slower option, but it is convenient when installing many tools.
Prepare the following environment.yml file:
| Code Block |
|---|
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 |
Create a new environment:
...
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:
...