pipeline-rnaseq

What problem does it solve?

This Skill streamlines the entire workflow of analyzing RNA sequencing data, generating accurate gene and transcript expression measures efficiently.

Core Features & Use Cases

• End-to-End Workflow: Processes raw FASTQ files through quality control, alignment, quantification, and signal track generation.
• Application Scope: Suitable for researchers and bioinformaticians conducting gene expression studies, transcript discovery, or preparing data for integrative analysis.
• Functional Requirements: Ensures compatibility with ENCODE standards, handles stranded libraries, supports multiple computational environments, and provides QC metrics.

Quick Start

Run the RNA-seq analysis pipeline on your FASTQ files by specifying your input files, genome, and annotation, then execute the main script with the appropriate profile.