Code

FASTQC

module load bioinfo-tools FastQC/0.11.9

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

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

# Load modules
module load bioinfo-tools
module load trimmomatic/0.39
# Your commands

trimmomatic PE -threads 2 /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/transcriptome/untrimmed/SRR6040095_scaffold_10.1.fastq.gz /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/transcriptome/untrimmed/SRR6040095_scaffold_10.2.fastq.gz -baseout /home/mathi/genome_analysis/durianproject/analyses/3_trim/3_trim_transcript/SRR6040095_scaffold_10.fq.gz ILLUMINACLIP:/sw/bioinfo/trimmomatic/0.39/snowy/adapters/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36