usage-guide.md

Ribosome Periodicity - Usage Guide

Overview

Validate Ribo-seq data quality by checking 3-nucleotide periodicity (the hallmark of active translation) and determining P-site offsets for accurate ribosome positioning.

Prerequisites

pip install plastid numpy matplotlib scipy

Quick Start

Tell your AI agent:

• "Check 3-nucleotide periodicity in my Ribo-seq data"
• "Determine P-site offset for my read lengths"
• "Create a metagene plot around start codons"
• "Validate my Ribo-seq library quality"

Example Prompts

Periodicity Validation

"Check if my Ribo-seq data shows 3-nt periodicity"

"Is my ribosome profiling library good quality?"

"Plot periodicity around start and stop codons"

P-site Offset

"Calculate optimal P-site offset for 28-30 nt reads"

"What offset should I use for my read length distribution?"

"Generate offset lookup table by read length"

Quality Assessment

"Create a metagene plot for my Ribo-seq"

"Compare periodicity between samples"

"What fraction of reads show clear periodicity?"

What the Agent Will Do

1. Load aligned Ribo-seq BAM file
2. Extract reads around annotated start codons
3. Calculate read density by position and frame
4. Quantify 3-nt periodicity (FFT or frame enrichment)
5. Determine optimal P-site offset per read length

Tips

• Strong periodicity in frame 0 indicates good library quality
• P-site offset varies by read length - calculate separately
• 12-13 nt offset is typical for 28-30 nt footprints
• Weak periodicity may indicate poor digestion or library issues
• Use annotated CDS for metagene analysis