BP4RNAseq

BP4RNAseq processes raw RNA sequencing (RNA-seq) reads to automate and standardize gene- and transcript-level quantification using integrated alignment-based and alignment-free workflows.

Key Features:

• Automated Workflow: Automates end-to-end processing of raw RNA-seq reads through a standardized pipeline.
• Minimal Input Requirements: Operates from two inputs: taxa name and NCBI accession codes for RNA-seq samples.
• Integration of Quantification Workflows: Integrates alignment-based and alignment-free quantification workflows to enhance sensitivity and accuracy.
• Comprehensive Output: Produces six formatted gene expression quantifications at both gene and transcript levels.
• Versatility in Application: Processes raw reads from both public (NCBI) and newly sequenced datasets and supports bulk and single-cell RNA-seq analyses.
• Reproducibility: Provides standardized automated processing to promote reproducible RNA-seq quantification.

Scientific Applications:

• Gene expression studies: Generates gene- and transcript-level expression quantifications for gene expression analysis.
• Comparative genomics/transcriptomics: Enables comparison of expression profiles across taxa or conditions using NCBI and newly generated datasets.
• Retrospective bulk RNA-seq analysis: Processes public NCBI RNA-seq datasets for retrospective bulk transcriptomic studies.
• Single-cell RNA-seq analysis: Supports gene- and transcript-level quantification for single-cell RNA-seq datasets.

Methodology:

Automated pipeline processes raw RNA-seq reads from public (NCBI) and newly sequenced datasets, accepts taxa name and NCBI accession codes as inputs, and applies integrated alignment-based and alignment-free quantification workflows to produce six formatted gene- and transcript-level expression quantifications.