Schizosaccharomyces-pombe-Chip-seq-analysis

After getting the bed file from the Peak calling, we can annotate and create all downstream analysis from two sets of data

Overview

This repository contains code and files related to ChIP-seq analysis. It includes scripts, peak files, and result images.

Files

• .gitignore: Specifies files and directories to be ignored by Git.
• C1_summits.bed: ChIP-seq peak summit file for condition C1.
• C2_summits.bed: ChIP-seq peak summit file for condition C2.
• Distribution of TF binding loci relative to TSS.png: Image showing the distribution of transcription factor (TF) binding loci relative to the transcription start site (TSS).
• Distribution of transcription factor-binding loci.png: Image showing the distribution of transcription factor-binding loci.
• Feature Distribution.png: Image showing the distribution of features.
• Feature Distribution1.png: Additional image showing the distribution of features.
• Feature Distribution2.png: Additional image showing the distribution of features.
• LICENSE: License file specifying the terms and conditions for using the code and files in this repository.
• Nanog-idr.png: Image showing the Nanog-idr peaks.
• Overlap of peaks and annotated genes.png: Image showing the overlap of peaks and annotated genes.
• PCF1.png: Image showing PCF1.
• PCF2.png: Image showing PCF2.
• PCF3.png: Image showing PCF3.
• README.md: This file, providing an overview and instructions for the repository.
• chip_seq_annotation.R: R script for ChIP-seq annotation and analysis.
• upset and vennypie.png: Image showing the upset plot and venn diagram using pie charts.
• upset.png: Image showing the upset plot.
• vennypie.png: Image showing the venn diagram using pie charts.

Usage

1. Clone or download the repository.
2. Install the necessary R packages specified in the code.
3. Place the ChIP-seq summit files (C1_summits.bed and C2_summits.bed) in the appropriate location.
4. Execute the chip_seq_annotation.R script for ChIP-seq annotation and analysis.
5. Refer to the generated images and results for further analysis and interpretation.

License

The code and files in this repository are licensed under LICENSE.

Note

This repository is provided as a reference for ChIP-seq analysis and may require customization or additional files/data for specific use cases.