Project Template – Simoes-Costa Lab

This repository provides a standard structure for computational projects in the Simoes-Costa Lab.

The goal of this template is to ensure that genomics analyses are organized in a consistent and reproducible way across projects, while remaining easy to understand and modify by lab members.

The template supports projects that may integrate multiple data types, including epigenomics, RNA-seq, and single-cell datasets.

Repository Structure

• metadata/ – project information, sample sheets, and data location notes
• single_cell/ – single-cell datasets and processed objects
• ATAC/ – ATAC-seq inputs and outputs
• CUT_RUN/ – CUT&RUN inputs and outputs
• RNA_Seq/ – RNA-seq inputs, alignments, and count matrices
• workflow/ – analysis scripts and configuration files
• results/ – final outputs such as figures, tables, and logs
• notebooks/ – exploratory analyses and visualization notebooks
• docs/ – project documentation and notes

Large sequencing files (FASTQ, BAM, etc.) should not be committed to GitHub.
Instead, store large datasets in institutional storage and document their locations in metadata/data_locations.md.

Usage

To start a new project:

1. Create a new repository from this template.
2. Update metadata/project_info.md with project details.
3. Add analysis scripts to workflow/.
4. Store final outputs in results/.

Update this README with the project-specific description, datasets, workflows, and outputs.