replicates-incorporation

To merge biological replicates for IDR-based consensus peak calling, you pool BAM files from chromatin assays and optionally split them into two balanced pseudo-replicates. This ensures reproducible peak analysis across more than two replicates.

Generating pseudo-replicates from pooled BAM files for ATAC-seq involves merging the biological replicates and then deterministically splitting the pooled reads into two balanced sets. This enables stable downstream peak calling and IDR analysis.

Yes, you can use IDR analysis on existing peak lists by operating in Peak mode. This mode skips BAM pooling and directly derives a conservative or optimal consensus peak set from the provided peak files.

You need more than two biological replicates for IDR-based consensus peak analysis when starting from BAM files. If you already have peak lists, two replicates are sufficient for merging into a consensus peak set.

The workflow selects its mode deterministically based on the provided data: it enters BAM mode for pre-peak calling pooling when raw BAMs are supplied, and switches to Peak mode for IDR analysis when pre-existing peak files are detected.

To ensure reproducibility when merging BAM files for ChIP-seq, the workflow enforces deterministic inputs and mode selection, outputting a structured project layout with merged and consensus peak sets for stable downstream analysis.