Alternative splicing(AS) is a biological process during gene expression that allows a single gene to code for multiple proteins.

The pipeline can automatically detect differential alternative splicing from RNA-Seq data. In this pipeline, both human and mouse species are supported. The pipeline consists of three analysis steps. Firstly, Trimmomatic or NGS QC Toolkit software was used for quality control. For reads after quality control, STAR software is used for mapping. Then, rMATS is used to detect differential alternative splicing events from RNA-Seq data.

The schematic diagram of RNA-seq-ASE-rMATS pipeline is as follows:

Software and references:
  • Trimmomatic: Trimmomatic: a flexible trimmer for Illumina sequence data.
  • NGS QC Toolkit: NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data.
  • STAR: STAR: ultrafast universal RNA-seq aligner.
  • rMATS: rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data.
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