modules/
rpbp_extractmetageneprofiles

Build per-read-length pileups of Ribo-seq read 5'-ends around annotated start codons - the "metagene profile". For each read length, the profile counts how many reads of that length have their 5' end at each position in a window around every annotated start codon, summed across all transcripts. Looking at the profile across the window reveals whether reads of that length show the 3-nucleotide periodicity characteristic of translating ribosomes.

This per-length view matters because different ribosome footprint lengths place the ribosomal P-site (the codon being decoded) at different offsets from the read's 5' end, so each length needs its own offset calibration. Output is consumed by rpbp/estimatemetagenebayesfactors, which scores each (length, offset) combination for periodicity.

rpbp metagene orf riboseq