SPARTA

SPARTA performs reference-based analysis of single-end Illumina bacterial RNA-seq data to process raw reads and produce gene feature counts and differential gene expression results for bacterial transcriptome studies.

Key Features:

• Supported data type: Single-end Illumina RNA sequencing (RNA-seq) data from bacterial transcriptomes.
• Comprehensive workflow: Integrates read trimming and adapter removal (Trimmomatic), quality control (FastQC), reference mapping (Bowtie), feature counting (HTSeq), and differential expression analysis (edgeR).
• Batch effect detection: Checks for potential batch effects within datasets to inform downstream differential expression analysis.
• Output generation: Produces quality analysis reports, gene feature count tables, differential gene expression tables, and scatterplots.

Scientific Applications:

• Differential gene expression: Identification of genes differentially expressed between experimental conditions in bacteria.
• Transcriptional response analysis: Characterization of bacterial transcriptional responses to stimuli or environmental changes.

Methodology:

Read trimming and adapter removal with Trimmomatic, quality control with FastQC, mapping to a reference genome with Bowtie, feature counting with HTSeq, differential expression analysis with edgeR, and checking for batch effects, producing quality reports, gene counts, differential expression tables, and scatterplots.