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	Classify transcript-level peaks as shared or specific between two condition peak tables.
4.9.3	serp_summary	Summarize one serp_peak result or one pairwise serp_overlap comparison, with summary tables and figures.
4.9.4	serp_plot	Draw SeRP enrichment profiles and called core peak regions for selected genes or transcripts.
4.9.5	serp_metaplot	Build a TIS/TTS metagene profile of SeRP enrichment for matched control/IP sample groups.
4.9.6	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 RPF density profiles (TXT/JSON/JSONL) to detect enriched binding or collision regions.
2. Run serp_overlap when you need to compare peaks shared or specific between two conditions.
3. Run serp_summary on a serp_peak or serp_overlap output prefix to generate summary tables and figures.
4. Run serp_plot to draw enrichment profiles and called core peak regions for selected genes or transcripts.
5. Run serp_metaplot to build a TIS/TTS enrichment metaplot over a transcript set shared by matched control/IP samples.
6. 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 (TXT) or JSON/JSONL density file with frame-specific sample columns.
serp_overlap	Two peak tables generated by serp_peak or compatible peak tables with required columns.
serp_summary	Output prefix of serp_peak (*_peaks.txt + *_peaks_ratio.txt) or serp_overlap (.summary.txt + .shared.peaks.txt + .shared.clusters.txt + .relationships.txt).
serp_plot	Output prefix of serp_peak (*_peaks.log + *_peaks_ratio.txt) plus a transcript ID/gene name or target list.
serp_metaplot	RPF density TXT/JSON/JSONL file plus matched control/IP sample groups.
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 compares all called peaks in two peak tables; the BHFDR column is used only when --max-fdr is specified.
• serp_summary detects peak versus overlap mode automatically from the input prefix; --mode is required when a prefix matches both output sets.
• serp_plot reads the reusable enrichment profile written by serp_peak; run serp_peak first so <prefix>_peaks.log and <prefix>_peaks_ratio.txt exist.
• serp_metaplot builds sample metaprofiles first and then aggregates matched IP/control enrichment across replicate pairs; --ck and --ip must contain equal numbers of samples.
• 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.