---
title: "Find Binding Motifs"
description: "Find Binding Motifs: an epigenomics recipe chaining epigenomics."
tags:
  - recipes
  - epigenomics
tools:
  - epigenomics
generated: true
source: quickActionConfig:chipseq-motif-pipeline
---

> **Generated recipe**

> Seeded from a curated quick-action prompt. The prompt below runs the real
> routing — copy it, change the target, and run.

> **Recommended pairing**

> These tools are commonly run together — they cover complementary ground on the same input.

**Best fit:** find binding motifs — an epigenomics goal.

**Try this prompt** — [open in a guest chat](/chat/new?guest=true&prompt=Run%20MACS3%20peak%20calling%20on%20ENCODE%20CTCF%20ChIP-seq%20in%20HepG2%20(ENCSR000AHD)%2C%20then%20use%20HOMER%20de%20novo%20motif%20discovery%20on%20the%20peaks%20-%20how%20does%20the%20discovered%20CTCF%20motif%20compare%20to%20the%20JASPAR%20consensus%20and%20which%20co-factor%20motifs%20are%20enriched%2C%20then%20recommend%20the%20top%20co-factor%20motif%20for%20a%20ChIP-seq%20validation%20experiment%20to%20identify%20liver-specific%20CTCF%20collaborating%20factors%3F).

> Run MACS3 peak calling on ENCODE CTCF ChIP-seq in HepG2 (ENCSR000AHD), then use HOMER de novo motif discovery on the peaks - how does the discovered CTCF motif compare to the JASPAR consensus and which co-factor motifs are enriched, then recommend the top co-factor motif for a ChIP-seq validation experiment to identify liver-specific CTCF collaborating factors?

_A real `chipseq-motif-pipeline` quick-action prompt — open it in a guest chat, then swap in your own compound or target._

## The prompt

```text
Run MACS3 peak calling on ENCODE CTCF ChIP-seq in HepG2 (ENCSR000AHD), then use HOMER de novo motif discovery on the peaks - how does the discovered CTCF motif compare to the JASPAR consensus and which co-factor motifs are enriched, then recommend the top co-factor motif for a ChIP-seq validation experiment to identify liver-specific CTCF collaborating factors?
```

## What each tool contributes

- [epigenomics](/docs/epigenomics) — ATAC-seq and ChIP-seq peak calling and differential analysis via MACS3
- **homer find motifs genome** — De novo and known motif enrichment in genomic regions

## Why these tools pair

MACS3 identifies enriched regions; HOMER discovers binding motifs in those peaks — the standard ChIP-seq analysis pipeline

## Data flow

Every tool operates on the same input: `bam_file`.

## Read next

- [Which tool?](/docs/which-tool) — match a single goal to a tool.
- [Workflows](/docs/workflows) — every workflow and recipe.
- [How the orchestrator picks tools](/docs/how-orchestration-works) — the same chain from a plain-language goal.