This pipeline utilizes Snakemake to perform RNA-seq analysis, including read alignment using STAR, quantification using Salmon, alternative splicing analysis using Darts. The pipeline is designed to handle multiple samples in parallel and automate the entire workflow from raw FASTQ files to TPM / alternative splicing results.

Paired-end reads are aligned to the reference genome using STAR.

Aligned reads are sorted and converted to BAM/ TranscriptomeBAM format.

Transcript quantification using Salmon to estimate gene expression levels.

RMATS counting: Counting of alternative splicing events (A5SS, A3SS, SE, RI) using Darts.

Bayesian inference: Statistical analysis of alternative splicing events to identify significant differences.

Gene-level differential expression analysis using DESeq2 to identify differentially expressed genes (DEGs) between conditions.