4.9 SeRP analysis

SeRP analysis contains RiboParser modules for selective translatome / SeRP-style peak analysis and sequence-property summaries.

These commands are part of the main workflow because they are specialized downstream analyses built around RiboParser RPF density output, rather than general file-format helper scripts.

Modules

Section	Command	Purpose
4.9.1	serp_peak	Detect enriched SeRP/IP peaks by comparing immunoprecipitation samples against control samples.
4.9.2	serp_overlap	Compare significant peak regions between mock-IP and flag-IP peak tables.
4.9.3	serp_properties	Calculate codon-usage and translated-protein properties from nucleotide FASTA sequences.

Recommended order

A typical SeRP analysis is organized as follows:

1. Run serp_peak on a merged RPF coverage table to detect enriched binding or collision regions.
2. Run serp_overlap when you need to compare significant peaks between mock-IP and flag-IP experiments.
3. Run serp_properties when you need codon-usage or translated-protein property summaries for CDS, ORF, or peak-associated sequences.

Input types

Different SeRP commands use different input files.

Command	Main input
serp_peak	RiboParser merged RPF coverage table with frame-specific sample columns.
serp_overlap	Two peak tables generated by serp_peak or compatible peak tables with required columns.
serp_properties	Nucleotide FASTA file containing coding sequences.

Notes

• serp_peak expects sample names provided to --ck and --ip to match the sample prefixes in the merged RPF table.
• serp_overlap is designed for comparing significant SeRP peak tables and uses the BHFDR column for significance filtering.
• serp_properties is sequence based. It does not take a SeRP peak table directly; prepare or retrieve FASTA sequences first if you want to summarize peak-associated sequences.