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Mathilda Stigenberg edited this page Apr 27, 2022
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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
Following the trimming of the untrimmed transcriptome with trimmomatic, a quality control of the recently trimmed trancriptome was done with the code below.
fastqc -o /home/mathi/genome_analysis/durianproject/analyses/4_fastqc/4_fastqc_transcriptome_trimmed/ -t 2 *.fq.gz
#!/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
#!/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
#!/bin/bash -l
#SBATCH -A uppmax2022-2-5
#SBATCH -M snowy
#SBATCH -p core
#SBATCH -n 2
#SBATCH -t 1:30:00
#SBATCH -J 5_mapping_bwa
#SBATCH -o mapping_bwa.output
#SBATCH --mail-type=ALL
#SBATCH --mail-user mathilda.stigenberg.5156@student.uu.se
# Load modules
module load bioinfo-tools
module load bwa/0.7.17
module load samtools/1.14
# Your commands
bwa index /home/mathi/genome_analysis/durianproject/analyses/2_assembly/ass_pb.contigs.fasta
bwa mem -t 2 /home/mathi/genome_analysis/durianproject/analyses/2_assembly/ass_pb.contigs.fasta /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/illumina_data/SRR6058604_scaffold_10.1P.fastq.gz /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/illumina_data/SRR6058604_scaffold_10.2P.fastq.gz > /home/mathi/genome_analysis/durianproject/analyses/5_mapping_bwa/aln_seq_bwa.sam
samtools sort /home/mathi/genome_analysis/durianproject/analyses/5_mapping_bwa/aln_seq_bwa.sam -o /home/mathi/genome_analysis/durianproject/analyses/5_mapping_bwa/aln_seq_bwa.bam
samtools index /home/mathi/genome_analysis/durianproject/analyses/5_mapping_bwa/aln_seq_bwa.bam /home/mathi/genome_analysis/durianproject/analyses/5_mapping_bwa/aln_seq_bwa.bai
#!/bin/bash -l
#SBATCH -A uppmax2022-2-5
#SBATCH -M snowy
#SBATCH -p core
#SBATCH -n 2
#SBATCH -t 3:00:00
#SBATCH -J 6_pilon
#SBATCH -o pilon.output
#SBATCH --mail-type=ALL
#SBATCH --mail-user mathilda.stigenberg.5156@student.uu.se
# Load modules
module load bioinfo-tools
module load Pilon/1.24
# Your commands
java -jar $PILON_HOME/pilon.jar --genome /home/mathi/genome_analysis/durianproject/analyses/2_assembly/ass_pb.contigs.fasta --bam /home/mathi/genome_analysis/durianproject/analyses/5_mapping_bwa/aln_seq_bwa.bam --outdir /home/mathi/genome_analysis/durianproject/analyses/6_improvement_pilon --threads 2
#!/bin/bash -l
#SBATCH -A uppmax2022-2-5
#SBATCH -M snowy
#SBATCH -p core
#SBATCH -n 2
#SBATCH -t 15:00
#SBATCH -J 7_quast
#SBATCH -o quast.output
#SBATCH --mail-type=ALL
#SBATCH --mail-user mathilda.stigenberg.5156@student.uu.se
# Load modules
module load bioinfo-tools
module load quast/5.0.2
# Your commands
python /sw/bioinfo/quast/5.0.2/snowy/bin/quast.py -t 2 -o /home/mathi/genome_analysis/durianproject/analyses/7_quality_assessment_quast -e /home/mathi/genome_analysis/durianproject/analyses/6_improvement_pilon/pilon.fasta
#!/bin/bash -l
#SBATCH -A uppmax2022-2-5
#SBATCH -M snowy
#SBATCH -p core
#SBATCH -n 2
#SBATCH -t 05:00
#SBATCH -J 8_multiqc
#SBATCH -o multiqc.output
#SBATCH --mail-type=ALL
#SBATCH --mail-user mathilda.stigenberg.5156@student.uu.se
# Load modules
module load bioinfo-tools
module load MultiQC/1.12
# Your commands
multiqc /home/mathi/genome_analysis/durianproject/analyses/1_fastqc/1_fastqc_illumina/*10* -o /home/mathi/genome_analysis/durianproject/analyses/8_multiqc/8_multiqc_illumina
multiqc /home/mathi/genome_analysis/durianproject/analyses/1_fastqc/1_fastqc_pacbio/*10* -o /home/mathi/genome_analysis/durianproject/analyses/8_multiqc/8_multiqc_pacbio
multiqc /home/mathi/genome_analysis/durianproject/analyses/1_fastqc/1_fastqc_transcriptome/trimmed/*10* -o /home/mathi/genome_analysis/durianproject/analyses/8_multiqc/8_multiqc_transcriptome/8_trimmed
multiqc /home/mathi/genome_analysis/durianproject/analyses/1_fastqc/1_fastqc_transcriptome/untrimmed/*10* -o /home/mathi/genome_analysis/durianproject/analyses/8_multiqc/8_multiqc_transcriptome/8_untrimmed
multiqc /home/mathi/genome_analysis/durianproject/analyses/4_fastqc/4_fastqc_transcriptome_trimmed/*10* -o /home/mathi/genome_analysis/durianproject/analyses/8_multiqc/8_multiqc_transcriptome/8_untrimmed_is_trimmed
#!/bin/bash -l
#SBATCH -A uppmax2022-2-5
#SBATCH -M snowy
#SBATCH -p core
#SBATCH -n 2
#SBATCH -t 1:00:00
#SBATCH -J 9_repeatmasker
#SBATCH -o repeatmasker.output
#SBATCH --mail-type=ALL
#SBATCH --mail-user mathilda.stigenberg.5156@student.uu.se
# Load modules
module load bioinfo-tools
module load RepeatMasker/4.1.2-p1
# Your commands
RepeatMasker -pa 2 -species malvaceae -dir /home/mathi/genome_analysis/durianproject/analyses/9_repeatmasker /home/mathi/genome_analysis/durianproject/analyses/6_improvement_pilon/pilon.fasta
#!/bin/bash -l
#SBATCH -A uppmax2022-2-5
#SBATCH -M snowy
#SBATCH -p core
#SBATCH -n 8
#SBATCH -t 30:00
#SBATCH -J 10_star
#SBATCH -o star.output
#SBATCH --mail-type=ALL
#SBATCH --mail-user mathilda.stigenberg.5156@student.uu.se
# Load modules
module load bioinfo-tools
module load star/2.7.9a
# Your commands
STAR --runThreadN 8 --runMode genomeGenerate --genomeDir /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_indexed_genome --genomeFastaFiles /home/mathi/genome_analysis/durianproject/analyses/9_repeatmasker/pilon.fasta.masked
STAR --runThreadN 8 --readFilesCommand zcat --genomeDir /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_indexed_genome/* --readFilesIn /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/transcriptome/trimmed/SRR6040092_scaffold_10.1.fastq.gz /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/transcriptome/trimmed/SRR6040092_scaffold_10.2.fastq.gz --outFileNamePrefix /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_mapping
STAR --runThreadN 8 --readFilesCommand zcat --genomeDir /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_indexed_genome/* --readFilesIn /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/transcriptome/trimmed/SRR6040093_scaffold_10.1.fastq.gz /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/transcriptome/trimmed/SRR6040093_scaffold_10.2.fastq.gz --outFileNamePrefix /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_mapping
STAR --runThreadN 8 --readFilesCommand zcat --genomeDir /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_indexed_genome/* --readFilesIn /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/transcriptome/trimmed/SRR6040094_scaffold_10.1.fastq.gz /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/transcriptome/trimmed/SRR6040094_scaffold_10.2.fastq.gz --outFileNamePrefix /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_mapping
STAR --runThreadN 8 --readFilesCommand zcat --genomeDir /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_indexed_genome/* --readFilesIn /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/transcriptome/trimmed/ SRR6040096_scaffold_10.1.fastq.gz /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/transcriptome/trimmed/SRR6040096_scaffold_10.2.fastq.gz --outFileNamePrefix /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_mapping
STAR --runThreadN 8 --readFilesCommand zcat --genomeDir /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_indexed_genome/* --readFilesIn /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/transcriptome/trimmed/SRR6040097_scaffold_10.1.fastq.gz /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/transcriptome/trimmed/SRR6040097_scaffold_10.2.fastq.gz --outFileNamePrefix /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_mapping
STAR --runThreadN 8 --readFilesCommand zcat --genomeDir /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_indexed_genome/* --readFilesIn /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/transcriptome/trimmed/SRR6156066_scaffold_10.1.fastq.gz /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/transcriptome/trimmed/SRR6156066_scaffold_10.2.fastq.gz --outFileNamePrefix /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_mapping
STAR --runThreadN 8 --readFilesCommand zcat --genomeDir /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_indexed_genome/* --readFilesIn /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/transcriptome/trimmed/SRR6156067_scaffold_10.1.fastq.gz /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/transcriptome/trimmed/SRR6156067_scaffold_10.2.fastq.gz --outFileNamePrefix /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_mapping
STAR --runThreadN 8 --readFilesCommand zcat --genomeDir /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_indexed_genome/* --readFilesIn /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/transcriptome/trimmed/SRR6156069_scaffold_10.1.fastq.gz /home/mathi/genome_analysis/durianproject/4_Tean_Teh_2017/transcriptome/trimmed/SRR6156069_scaffold_10.2.fastq.gz --outFileNamePrefix /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_mapping
STAR --runThreadN 8 --readFilesCommand zcat --genomeDir /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_indexed_genome/* --readFilesIn /home/mathi/genome_analysis/durianproject/analyses/3_trim/3_trim_transcript/SRR6040095_scaffold_10_1P.fq.gz /home/mathi/genome_analysis/durianproject/analyses/3_trim/3_trim_transcript/SRR6040095_scaffold_10_2P.fq.gz --outFileNamePrefix /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_mapping
STAR --runThreadN 8 --readFilesCommand zcat --genomeDir /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_indexed_genome/* --readFilesIn /home/mathi/genome_analysis/durianproject/analyses/3_trim/3_trim_transcript/SRR6040095_scaffold_10_1U.fq.gz /home/mathi/genome_analysis/durianproject/analyses/3_trim/3_trim_transcript/SRR6040095_scaffold_10_2U.fq.gz --outFileNamePrefix /home/mathi/genome_analysis/durianproject/analyses/10_star_mapping/10_mapping