mRNA-seq (NGS) with reference genome

mRNA sequencing allows profiling of all mRNA transcripts in cells under specific conditions and is a widely adopted technology in multiple research areas. The BMKCloud mRNA-seq (with a reference genome) pipeline is designed to analyze poly-A enriched sequencing libraries when a high-quality and well-annotated reference genome is available. The pipeline starts with quality control based on sequencing quality and read alignment against the reference genome, followed by transcript assembly. Sequence structure analysis provides information on alternative splicing and novel genes. The differential expression analysis finds differentially expressed genes (DEGs) among the tested conditions, followed by functional annotation and enrichment of DEGs to extract biological insights.