bio-splicing-pipeline

You can perform differential splicing analysis with rMATS-turbo directly on RNA-seq FASTQ files. The pipeline handles STAR 2-pass alignment and junction quality control automatically before running the differential testing.

The best way to run junction saturation checks for alternative splicing analysis is through an end-to-end pipeline that integrates quality control after STAR 2-pass alignment. This ensures robust junction discovery and quantification before differential testing.

Yes, you can generate Sashimi plots for condition-specific splice events from RNA-seq data. The pipeline produces Sashimi plot visualizations and standardized reports for publication-ready results after identifying top differential splicing candidates.

Yes, this RNA-seq splicing analysis pipeline supports optional IsoformSwitchAnalyzeR analysis. It integrates this tool alongside rMATS-turbo differential testing to generate robust results and support downstream interpretation.

You can use raw FASTQ files for rMATS-turbo differential splicing testing because the pipeline performs STAR 2-pass alignment first. It processes FASTQ inputs end-to-end to produce standardized outputs for reproducibility.

STAR 2-pass alignment is used for alternative splicing quantification to improve junction discovery and accuracy. It maps RNA-seq reads across splice junctions more comprehensively before rMATS-turbo tests for differential events.