This repository contains scripts and resources for the analysis of DAP-seq (DNA Affinity Purification Sequencing) data. DAP-seq is a high-throughput technique used to identify DNA-binding sites of transcription factors and other DNA-binding proteins across the genome.
The analysis pipeline includes preprocessing of raw sequencing data, alignment to the reference genome, peak calling, peak annotation, and downstream functional analysis of identified binding sites.
- Python 3.x
- R (with Bioconductor packages)
- Bowtie2 or BWA
- MACS2
- Samtools
- Bedtools
- FastQC
- MultiQC
- IGV
- ChIPseeker
- HOMER
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Clone the Repository:
git clone https://github.com/arbazattar11/DAPseq
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Install Dependencies:
Ensure that all required dependencies listed above are installed and configured properly on your system.
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Preprocessing:
- Preprocess raw sequencing data (FASTQ files) using FastQC 68ED for quality assessment and Trimmomatic for adapter trimming and quality filtering.
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Alignment:
- Map cleaned reads to the reference genome using Bowtie2 or BWA.
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Peak Calling:
- Identify enriched regions (peaks) using MACS2.
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Peak Annotation:
- Annotate identified peaks with nearby genes using ChIPseeker.
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Functional Analysis:
- Perform downstream functional analysis to understand the biological significance of identified binding sites.
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Visualization:
- Visualize the ChIP-seq data and identified peaks using IGV or other genome browsers.
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Documentation:
- Document the analysis steps, parameters used, and results obtained for reproducibility.
This project is licensed under the MIT License.
Contributions to improve and extend this analysis pipeline are welcome. Please fork the repository, make your changes, and submit a pull request.
- This analysis pipeline was inspired by various resources and previous studies in the field of genomics and bioinformatics.
- We acknowledge the developers and maintainers of the software tools and libraries used in this pipeline.
For questions or inquiries, please contact Arbaz.