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Install tools using conda
Create a conda
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environments
Create a conda environment called ONTvariants_QCnanoplot
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conda create -n ONTvariants_QC |
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Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.12.0 latest version: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/barrero/miniconda3/envs/ONTvariants_QCnanoplot Proceed ([y]/n)? y Preparing transaction: done Verifying transaction: done Executing transaction: done # # To activate this environment, use # # $ conda activate ONTvariants_QCnanoplot # # To deactivate an active environment, use # # $ conda deactivate |
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conda activate ONTvariant_QCnanoplot |
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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#!/bin/bash -l #PBS -N run1_QC #PBS -l select=1:ncpus=8:mem=16gb #PBS -l walltime=7248:00:00 #PBS -m abe cd $PBS_O_WORKDIR conda activate ONTvariants_QC ############################################################### # Variables ############################################################### FASTQ='/work/training/ONTvariants/data/SRR17138639_1.fastq.gz' GENOME='/work/training/ONTvariants/data/chr20.fasta' SAMPLEID='SRR17138639' ############################################################### #STEP1: NanoPlot - overall QC report NanoPlot -t 8 --fastq $FASTQ --prefix ${SAMPLEID}_QC_ --plots dot --N50 --tsv_stats #STEP2: porechop_abi - remove adapters porechop_abi -abi -t 8 --input ${SAMPLEID}.fastq.gz --discard_middle --output ${SAMPLEID}_trimmed.fastq #STEP3: chopper - retain reads with >Q10 and length>300b chopper -q 10 -l 300 -i ${SAMPLEID}_trimmed.fastq > ${SAMPLEID}_trimmed_q10.fastq |
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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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