Gene Regulatory Dynamics During the Development of Cloeon dipterum

This repository contains the code and analysis pipeline associated with the paper "Gene regulatory dynamics during the development of a paleopteran insect, the mayfly Cloeon dipterum." The repository is structured into two main sections: ATAC Pipeline and Downstream Analysis.

ATAC Pipeline

The ATAC pipeline processes ATAC-seq data to identify consensus peaks and associates these peaks with genomic zones.

ATAC-seq Mapping and Peak Calling

The ATAC_pipe.pl script is used for mapping reads using Bowtie2. Peak calling is conducted with the idr_ATAC_script.sh, which employs MACS2 for peak detection and IDR analysis. For more detail, see here.

Peak Classification and Gene Assignment

Peaks are classified and linked to genes based on proximity to Transcription Start Sites (TSS). The cisreg_map.py script maps these peaks to genes. For more detail, see here.

Downstream Analysis

This section encompasses various analyses related to chromatin accessibility during different embryonic stages of C. dipterum:

1. Genomic Peaks Analysis & Comparative Distribution
2. Differential Chromatin Accessibility Analysis
3. Chromatin Changes in Relation to WGCNA Modules
4. Chromatin Dynamics with Mfuzz Clustering
5. Chromatin Dynamics with Kmeans Clustering
6. Integrative Analysis of RNA-seq and ATAC-seq Data

Contact

For further inquiries, please contact:

• Maria Rossello: mariarossello@ub.edu
• Isabel Almudi: ialmudi@ub.edu