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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.

Suggested directory structure

The SeRP modules are organized under sce/6.serp/ (see the project layout in 3 New project). Create the SeRP sub-directories (01.peak to 06.properties, matching sections 4.9.1-4.9.6 above) as follows:

mkdir -p 01.peak 02.overlap 03.summary 04.peak_plot 05.metaplot 06.properties

Input dependency

The density-based SeRP commands consume the merged RPF density matrix produced by rpf_Merge in 05.merge of the Ribo-seq branch (sce/4.ribo-seq/5.riboparser/05.merge, see 4.5.5 Merge density); the sample names passed to --ck and --ip must match the sample prefixes in that file. Inside SeRP, the commands form a chain: run serp_peak first, then serp_overlap, serp_plot, and serp_summary on its outputs, and optionally serp_properties on the serp_summary overlap classification. The per-module input and output are summarized below:

Section Main input Main output
Peak (4.9.1) merged RPF density (TXT/JSON/JSONL) and control/IP sample names peak tables, BED regions, peak sequences, and enrichment-ratio tables
Overlap (4.9.2) two peak tables generated by serp_peak shared/specific peak classification and relationship tables
Summary (4.9.3) output prefix of serp_peak or serp_overlap summary tables and figures
Peak plot (4.9.4) serp_peak output prefix and a target gene/transcript or target list per-target enrichment-profile figures
Metaplot (4.9.5) merged RPF density and matched control/IP sample groups TIS/TTS metaplot tables and figures
Properties (4.9.6) nucleotide FASTA; optional serp_summary overlap classification (-p) sequence QC, codon-usage, and protein-property tables and figures

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.