4.9.2 SeRP overlap

serp_overlap

serp_overlap compares significant peak regions between mock-IP and flag-IP peak result tables.

Function

Use this command when you want to:

• compare two SeRP peak result tables;
• identify peaks that overlap on the same transcript;
• label peaks as mock-IP specific, flag-IP specific, or overlapping;
• draw Venn diagrams for gene-level and peak-region overlap.

Input

The command takes two peak tables:

Input	Description
Mock-IP peak table	Peak result table from mock-IP or control-like SeRP analysis.
Flag-IP peak table	Peak result table from flag-IP or IP SeRP analysis.

The input tables should contain at least the following columns:

transcripts  peak_start  peak_end  BHFDR

Only peaks with BHFDR < 0.05 are retained for overlap analysis.

Parameters

Parameter	Required	Meaning
-m	yes	Input mock-IP peak file in TXT/TSV format.
-f	yes	Input flag-IP peak file in TXT/TSV format. Although the parser marks it as optional, the implementation reads and checks this file, so provide it.
--om	yes	Output prefix for the mock-IP overlap table.
--of	yes	Output prefix for the flag-IP overlap table.

Output

Output	Description
<mock_prefix>.overlap.txt	Mock-IP significant peak table with an added overlap annotation column.
<flag_prefix>.overlap.txt	Flag-IP significant peak table with an added overlap annotation column.
<mock_prefix>_vs_<flag_prefix>_venn.pdf	Venn diagram comparing significant genes and peak regions.
<mock_prefix>_vs_<flag_prefix>_venn.png	PNG version of the Venn diagram.

The overlap column is annotated as:

Value	Meaning
overlap	The peak overlaps a significant peak from the other table on the same transcript.
mock-IP	The peak is specific to the mock-IP table.
flag-IP	The peak is specific to the flag-IP table.

Examples

Compare mock-IP and flag-IP peak tables:

serp_overlap \
  -m mock_peaks.txt \
  -f flag_peaks.txt \
  --om mock \
  --of flag

Compare two peak tables generated by serp_peak:

serp_overlap \
  -m SeRP_mock_peaks.txt \
  -f SeRP_flag_peaks.txt \
  --om SeRP_mock \
  --of SeRP_flag

Notes

• The command filters both input tables by BHFDR < 0.05 before overlap analysis.
• Peaks are compared only within the same transcript.
• Two peaks are considered overlapping when their coordinate intervals intersect.
• In the current implementation, it is safer to always provide both --om and --of. The fallback prefix handling is not reliable when these arguments are omitted.