Bug fixes and improvements:
- Fix Step 18: use merged SAF for meta-gene featureCounts (eliminates cross-region read pair double-counting)
- Remove ENCODE blacklist from meta-gene counting (retain for deeptools density plots only)
- Fix undefined variable sample_dir in Step 27 HTML report
- Fix hardcoded thread counts in Step 26 density plot scripts
- Fix percentage denominator in Step 24 QC matrix
- Remove unused imports across 5 Python scripts
- Consolidate 7 individual SAF files into single merged meta-gene SAF (801,166 features) and update the compressed HG38 annotation files into Zenodo https://zenodo.org/records/19171865