bio-ribo-seq-ribosome-stalling

Calculate Codon-Level Occupancy

Goal: Quantify ribosome occupancy at each codon position across all transcripts.

Approach: Map reads to P-sites using a fixed offset, then bin counts into codons along each CDS.

Identify Pause Sites

Goal: Detect codon positions with significantly elevated ribosome occupancy indicative of translational pausing.

Approach: Z-score normalize occupancy per transcript and flag positions exceeding a threshold (default z > 3).

Codon-Specific Occupancy

Goal: Calculate average ribosome occupancy for each of the 64 codon types across all genes.

Approach: Aggregate read density per codon identity across all CDS positions and compute per-codon mean occupancy.