Validate Ribo-seq library quality by measuring 3-nucleotide periodicity (the signature of genuine elongating ribosomes) and calibrating read-length-specific P-site offsets. Periodicity is both the QC gate that decides whether the data is interpretable at codon level and the prerequisite calibration for ORF detection, translation efficiency, and stalling analysis.
# R (primary path)
install.packages("riboWaltz") # or BiocManager / devtools from GitHub
# Python alternative
pip install plastid numpy scipy pysam
Tell your AI agent what you want to do: - "Check 3-nucleotide periodicity in my Ribo-seq data" - "Calibrate P-site offsets per read length with riboWaltz" - "Decide which read lengths to keep for downstream analysis" - "Make a metagene/metaheatmap around start codons"
"Does my Ribo-seq library show 3-nt periodicity, and what is the frame-0 fraction?"
"Is my library good enough for ORF calling, or only for gene-level counts?"
"Why does my bacterial library look aperiodic?"
"Calibrate P-site offsets for each read length with riboWaltz"
"Get offsets with plastid's metagene and psite scripts instead of R"
"Which read lengths should I drop because they lack periodicity?"
"Make a metaprofile and metaheatmap around start and stop codons"
"Compare frame-0 fraction across my samples"
"Score periodicity from the CDS body, not the start peak"