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Mathilda Stigenberg edited this page Apr 8, 2022 · 35 revisions

FASTQC

module load bioinfo-tools FastQC/11.0.9

fastqc -o /home/mathi/genome_analysis/durianproject/analyses/1_fastqc_illumina/ -t 2 *.fastq.gz

fastqc -o /home/mathi/genome_analysis/durianproject/analyses/2_fastqc_pacbio/ -t 2 *.fq.gz

fastqc -o /home/mathi/genome_analysis/durianproject/analyses/3_fastqc_transcriptome/trimmed/ -t 2 *.fastq.gz

fastqc -o /home/mathi/genome_analysis/durianproject/analyses/3_fastqc_transcriptome/untrimmed/ -t 2 *.fastq.gz

CANU

#!/bin/bash -l #SBATCH -A uppmax2022-2-5 #SBATCH -M snowy #SBATCH -p core #SBATCH -n 4 #SBATCH -t 19:00:00 #SBATCH -J 2_assembly_pacbio #SBATCH --mail-type=ALL #SBATCH --mail-user mathilda.stigenberg.5156@student.uu.se

Load modules

module load bioinfo-tools module load canu/2.2

Your commands

canu -d /home/mathi/genome_analysis/durianproject/analyses/2_assembly -p ass_pb genomeSize=24m useGrid=False corThreads=4 -pacbio /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/pacbio_data/SRR6037732_scaffold_10.fq.gz

TRIMMOMATIC

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