bio-splicing-qc

Junction Saturation Analysis

Goal: Determine whether sequencing depth is sufficient for comprehensive splicing detection.

Approach: Run RSeQC junction saturation on BAM files and check whether the junction discovery curve reaches a plateau.

"Assess RNA-seq quality for splicing analysis" -> Evaluate junction saturation, junction novelty rate, splice site strength, and read coverage.

• Python/CLI: junction_saturation.py, junction_annotation.py (RSeQC)
• Python: maxentpy for splice site scoring, pysam for junction read counting

## Run junction saturation for multiple samples

samples = ['sample1.bam', 'sample2.bam', 'sample3.bam']

for sample in samples:
    subprocess.run([
        'junction_saturation.py',
        '-i', sample,
        '-r', 'annotation.bed',
        '-o', sample.replace('.bam', '_junc_sat')
    ], check=True)

## Junction Annotation

**Goal:** Classify observed junctions as known, partially novel, or completely novel relative to annotation.

**Approach:** Run RSeQC junction annotation and compute the ratio of known to novel junctions as a data quality indicator.

```bash