# inter3D

**Repository Path**: hi-c_baseline/inter3D

## Basic Information

- **Project Name**: inter3D
- **Description**: https://github.com/bm2-lab/inter3D
- **Primary Language**: Unknown
- **License**: GPL-3.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2026-03-11
- **Last Updated**: 2026-03-11

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# Inter3d:  A ready-to-use pipeline for CTCF-mediated interactome identification with 3D genomics and high-throughput sequencing
-------------

## Data required
- samples/cells of two or more conditions.
- RNA-seq,  HiC and CTCF ChIP-seq, ATAC-seq or DNase-seq required.
- H3K4me3 and H3K27ac ChIP-seq. (optional)

## Inter3d biology mechanism
![inter3d mechanism](mech.png)


## Inter3d workflow
- **Before Inter3d**
1. Preprocessing RNA-seq
- Mapping and gene quantification. (not included)
- DEG identification.(not included)
2. Preprocessing ChIP-seq and ATAC-seq
- Mapping to reference genome.(not included)
- Consensus peak calling.(not included)  
3. Preprocessing Hi-C.

** We recommend using ENCODE uniform processing pipeline for your raw data preprocessing. [https://www.encodeproject.org/pipelines/](https://www.encodeproject.org/pipelines/)

- **Using Inter3d**
4. Identify CTCF-mediated TAD alterations.
5. Identify candidate genes regulated by CTCF binding.
6. Find Enhancer-Promoter pairs regulated by CTCF binding.

## Inter3d quick guide
- Input files:
  - DEG list with Log2FoldChange of Case1/Case2
  - ATAC-seq/DNase-seq peaks in Case1 and Case2 
  - CTCF ChIP-seq peaks in Case1 and Case2 
  - Genome-wide TAD boundary of Case1 and Case2

- Output files:
  - Genome coordinates of candidate enhancers and linked promoters.
    - for etc: ctcf_gain_case1_high_gene_CRE.xls
  - Genome coordinates of candidate CTCF binding sites.
    - for etc: ctcf_gain_case1_high_gene.xls
    
**Run Inter3d with demo dataset used in manuscript**  
```bash
cd demo
bash run_demo.sh
```

Reference:  
Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription. Genomics, Proteomics & Bioinformatics. 2024 (online)