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ribosome-stalling

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Detect ribosome pausing and stalling at codon resolution from Ribo-seq, using local-relative occupancy metrics and A-site assignment. Use when studying elongation dynamics, codon dwell times, pause motifs, or ribosome collisions, and when judging whether a pause is real biology or a cycloheximide artifact.

When to use

• Detect ribosome pause sites
• Study elongation dynamics
• Analyze codon dwell times
• Identify pause motifs
• Detect ribosome collisions
• Judge if pause is real biology or drug artifact
• Calculate A-site codon density
• Score pauses with local-relative metric

When not to use

• Initiation-site mapping
• Harringtonine/lactimidomycin data analysis
• CHX pre-incubation codon dwell time reporting
• CHX pre-incubation tRNA correlation reporting

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