High-Throughput-Analysis of the Spinacia oleracea L. Genome

Credits

This analysis was performed by Anne-Sophie Chys and Ruben Olbrechts as a part of a project of High Throughput analysis at the Howest University of Applied Sciences.

Introduction

This repository contains the scripts and data used for analyzing the Spinacia oleracea L. genome. The SP75 Genome data was obtained from the SpinachBase. The goal of the performed Tigh-Throughput transcriptomics (HTTr) is to compare differentially expressed transcripts from experimental data. Root and tissue samples where available and treated with replete and deplete conditions of nitrogen during growth. RNA-Sequencing (RNA-Seq) is later used to analyse the differentially expressed genes (DEGs). The samples that where used came from the Gene Expression Omnibus (GEO) from Series GSE145943.

Tools

The following tools were used for this analysis:

• Quality control: FastQC (v0.11.9) & MultiQC (v1.13)
• Trimming: Trimmomatic (v0.39)
• Index building: Hisat2 (v2.2.1)
• Mapping: Hisat2 (v2.2.1)
• Filtering, sorting and indexing: SAMtools (v1.9)
• Counting: HTSeq (v0.12.3)
• Differential expression analysis: EdgeR (v3.36.0)

Data

The raw fastq files were first trimmed using Trimmomatic and the resulting files were then used for alignment and quantification.

Scripts

The scriptsdirectory contains the following scripts used for the analysis:

differential_expression_trimmed.sh: differential_expression_untrimmed.sh:

Results

Usage

To reproduce the analysis, clone this repository and run the scripts in the following order:

1. hisat2_alignment: Align the reads to the SP75 genome.
2. featurecounts_quantification: Quantify the expression levels of the genes.
3. multiqc_report: Generate a report of the analysis results.

References

• SpinachBase: https://spinachbase.org/
• HISAT2: https://ccb.jhu.edu/software/hisat2/index.shtml
• FeatureCounts: http://subread.sourceforge.net/
• MultiQC: https://multiqc.info/