Description

Build a per-ORF P-site count vector for every candidate open reading frame (ORF) in the catalogue. For each ORF, walks the spliced exons in 3-nucleotide codon steps and counts the P-site positions (read 5'-end coordinate plus the length-specific offset selected upstream) that fall in each codon. Counts are summed across all read lengths that passed the periodicity filter from rpbp/getperiodiclengthsoffsets.

The resulting per-ORF vectors are the input to Bayesian translation scoring in rpbp/estimateorfbayesfactors: a translated ORF should show P-site density concentrated at codon-start positions, while a non-translated region should look flat or noisy. Emitted as a sparse matrix (one row per ORF, columns indexed by codon position).

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Tools

rpbp Documentation

Rp-Bp - Bayesian inference of ribosome profiling data for identifying translated open reading frames

https://github.com/dieterich-lab/rp-bpdoi: 10.1093/nar/gkw1350License: MIT
Authors