consensus_peaks.md

Consenrich → Consensus Peak Calling

• Consenrich can be paired with peak callers such as ROCCO to call consensus peaks given multiple HTS data.
• Methods based in pattern-matching or the continuous wavelet transform (CWT) may also be effective.

We provide some casual examples below for ATAC-seq and ChIP-seq.

ATAC-seq

ChIP-seq

Users wishing to apply ROCCO to Consenrich ChIP-seq results may find it worthwhile to tune ROCCO's --budget parameter and/or run with --narrowPeak to filter peaks based on $p$-values post hoc. A dedicated ChIP-seq/Cut&Run mode for ROCCO is upcoming to mitigate dependence on fine-tuning or filtering results after the fact.