ChIP-seq¶

ChIP runs remove duplicates by default and supports feature definitions matched to distinct signal geometries.

--broad-mode	Intended signal	Feature strategy
off	transcription factors and narrow marks	narrow MACS3 plus IDR by default
domain	broad domains	MACS3 broad peaks with replicate support
genebody	gene-body-associated marks	annotation-derived gene bodies
diffuse	very diffuse chromatin signal	fixed genomic bins

# Narrow / TF-like
omnomnomics chip -i EXPERIMENT -g GRCh38 -m metadata.tsv --broad-mode off

# Broad domains
omnomnomics chip -i EXPERIMENT -g GRCh38 -m metadata.tsv --broad-mode domain

# Gene-body signal
omnomnomics chip -i EXPERIMENT -g GRCh38 -m metadata.tsv --broad-mode genebody

# Diffuse signal
omnomnomics chip -i EXPERIMENT -g GRCh38 -m metadata.tsv --broad-mode diffuse

Use -I to provide the matching input/control BAM where appropriate. ChIP feature construction runs at step 10 and post-DE interpretation at step 15.

Narrow and transcription-factor ChIP¶

--narrow-peak-strategy idr is the default and derives reproducible peaks from separate biological-replicate calls. --idr-mode encode adds pseudoreplicate diagnostics; basic uses true replicates only. For groups with more than two replicates, --idr-pairing-policy all_pairs evaluates every pair, while anchor_vs_all compares the first replicate with each remaining replicate.

The alternative --narrow-peak-strategy macs3 enables --chip-peak-opt-mode:

Mode	Candidate calls per group
none	one model-based MACS3 call at q=0.01
fast	model-based calls at q=0.01 and q=0.001
full	the two model-based calls plus fixed shift/extension calls at -75/150 and -100/200 for both q-values

For fast and full, omnomnomics calls each candidate on both pooled and replicate BAMs. It selects the candidate using a documented composite score: 45% replicate peak-set agreement, 35% FRiP, 15% low blacklist overlap, and 5% preference for a median peak width near 250 bp. Full candidate tables, selected parameters, and diagnostic plots are retained under chip_narrow_peak_call_optimization/. This optimization is useful when a MACS3-only peak set is required; IDR remains the preferred default for replicated TF ChIP-seq.

Broad-domain ChIP¶

--broad-mode domain calls broad MACS3 domains and filters them by replicate support. The principal controls are:

Control	Purpose
--chip-broad-qvalue	relaxed q-value used for pooled, replicate, and pooled-pseudoreplicate MACS3 calls
--chip-broad-cutoff	MACS3 significance cutoff used to link nearby enriched regions into broad domains
--chip-broad-min-length	optional minimum domain length passed to MACS3
--chip-broad-max-gap	optional maximum gap that MACS3 may bridge within a domain
--chip-broad-replicate-fraction	minimum fraction of biological replicates that must support a pooled domain
--chip-broad-overlap-fraction	minimum reciprocal overlap used to count replicate support

The defaults require support from every replicate and at least 50% reciprocal overlap. Relaxing these values increases sensitivity but also admits less reproducible domains.

Gene-body and diffuse ChIP¶

--broad-mode genebody quantifies annotation-derived gene bodies instead of calling peaks. --broad-mode diffuse partitions the genome into fixed bins, with bin-size and merge-gap controls for signals that do not form discrete domains. These modes change the feature definition used for counting and differential analysis; they are not merely plotting choices.

The SPP gate has the same behavior as for ATAC: none disables gating, warn reports flags, drop removes flagged samples from downstream analysis, and strict aborts on any threshold failure.