This is a README-file concerning paper 4, the one about the durian fruit. The durian fruit is analyzed by assembling its genome, doing annotation and expression analysis. The pipeline for doing these analyses is explained below so one can remake this project and follow the correct order when running the scripts.

FastQC

FastQC is used for doing a quality check on the raw data.

This can be done in the interactive session by writing the commands below.

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

If one is following this pipeline, one can of course choose their own output directory where to store the results.

MultiQC

MultiQC is used for combining the results from FastQC into one summary report.

The script for doing this is called 8_multiqc.sh and can be found in the directory: /home/mathi/genome_analysis/durianproject/code

CANU

CANU is used for assemble a genome with reads as input.

The script for doing this is called 2_assembly_pacbio.sh and can be found in the directory: /home/mathi/genome_analysis/durianproject/code

Trimmomatic

Trimmomatic is used for trimming untrimmed transcriptomic reads.

The script for doing this is called 3_trimming_transcriptome.sh and can be found in the directory: /home/mathi/genome_analysis/durianproject/code

Therafter, a quality report can be obtained for this newly trimmed data by doing this command below in the interactive session.

module load bioinfo-tools FastQC/0.11.9
fastqc -o /home/mathi/genome_analysis/durianproject/analyses/4_fastqc/4_fastqc_transcriptome_trimmed/ -t 2 *.fq.gz 

BWA

BWA is used for mapping illumina reads against the assembled genome.

The script for doing this is called 5_mapping_bwa.sh and can be found in the directory: /home/mathi/genome_analysis/durianproject/code

Pilon

Pilon is used for correcting the assembly.

The script for doing this is called 6_pilon.sh and can be found in the directory: /home/mathi/genome_analysis/durianproject/code

QUAST

QUAST is used for doing a quality check on the assembled genome.

The script for doing this is called 7_quast.sh and can be found in the directory: /home/mathi/genome_analysis/durianproject/code

RepeatMasker

RepeatMasker is used for masking the repeats in the genome.

The script for doing this is called 9_repeatmasker.sh and can be found in the directory: /home/mathi/genome_analysis/durianproject/code

STAR

STAR is used for mapping the trimmed transcriptomic reads to the assembled masked genome.

The script for doing this is called 10_star.sh and can be found in the directory: /home/mathi/genome_analysis/durianproject/code

BRAKER

BRAKER is used for doing a structural annotation of the genome.

The script for doing this is called 11_braker.sh and can be found in the directory: /home/mathi/genome_analysis/durianproject/code

However, before running the script one needs to run the following commands below.

module load bioinfo-tools
module load augustus/20200915-ed0cb90

source $AUGUSTUS_CONFIG_COPY

chmod a+w -R /home/mathi/genome_analysis/durianproject/analyses/11_braker_annotation/augustus_config/species/
cp -vf /sw/bioinfo/GeneMark/4.33-es/snowy/gm_key $HOME/.gm_key 

EggNOGmapper

EggNOGmapper is used for doing a functional annotation of the genome.

The script for doing this is called 12_eggnogmapper.sh and can be found in the directory: /home/mathi/genome_analysis/durianproject/code

HTseq

HTseq is used for differential expression analysis by counting how many genes each transcriptomic read map to.

The script for doing this is called 13_htseq.sh and can be found in the directory: /home/mathi/genome_analysis/durianproject/code

DESeq2

DESeq2 is used for doing differential expression analysis by plotting a PCA plot visualizing how the transcriptomic data differ in expression and a heatmap visualizing how varied the genes are in expression level.

The script for doing this is called 14_deseq2.r and can be found in the directory: /home/mathi/genome_analysis/durianproject/code

However, it is best to run this script in Rstudio and run these commands below before running the script, in order to install the package DESeq2.

if (!require("BiocManager", quietly = TRUE))
	install.packages("BiocManager")
BiocManager::install("DESeq2")