RseqFlow

RseqFlow processes single-ended Illumina RNA-Seq reads to perform quality control, generate mapped-read signal tracks, calculate gene expression levels, identify differentially expressed genes, and call coding single nucleotide polymorphisms (SNPs) for downstream genomics and transcriptomics analyses.

Key Features:

• Single-ended Illumina RNA-Seq support: Processes single-ended Illumina RNA-Seq reads as input data.
• Quality Control (QC): Performs quality control on sequencing reads to filter and assess read quality prior to downstream analysis.
• Signal Tracks of Mapped Reads: Generates signal tracks for mapped reads to represent read distribution across the genome.
• Expression Level Calculation: Calculates gene expression levels from RNA-Seq data for quantitative analysis.
• Differentially Expressed Genes Identification: Identifies differentially expressed genes between experimental conditions.
• Coding SNPs Calling: Calls coding single nucleotide polymorphisms (SNPs) from RNA-Seq data.

Scientific Applications:

• Genomics: Enables detection of coding SNPs and expression quantification to support genomics investigations.
• Transcriptomics: Supports transcriptomic analyses including expression-level quantification and differential expression studies.
• Systems Biology: Provides expression and variant outputs usable for systems biology studies linking gene expression and genetic variation to biological processes.

Methodology:

RseqFlow leverages the Pegasus Workflow Management System to formalize and manage the analysis workflow, mapping analysis modules onto available computational resources, enforcing execution order, and automating task supervision.