This repository contains the analytical pipeline for the MAXOMOD project, which focuses on the multi-omic analysis of axono-synaptic degeneration in the motor neuron disease amyotrophic lateral sclerosis (ALS). The project explores sex differences and molecular subclusters in ALS and investigates the MAPK pathway as a potential therapeutic target. For a detailed understanding of the scientific background and the findings, refer to our paper published on [Nature Communications](https://www.nature.com/articles/s41467-024-49196-y). ## Table of Contents - [Getting Started](#getting-started) - [Prerequisites](#prerequisites) - [Data Preparation](#data-preparation) - [Organize Data](#organize-data) - [Reproducing Results](#reproducing-results) - [Contributing](#contributing) - [Collaboration](#collaboration) ## Getting Started ### Prerequisites - Git - [DVC](https://dvc.org/) - [Nextflow](https://www.nextflow.io/) - Container execution engine (e.g. [Docker](https://www.docker.com/) or [Podman](https://podman.io/)) Clone the git repository: ``` git clone https://github.com/imsb-uke/MAXOMOD_Pipeline.git ./maxomod ``` Enter the cloned directory: ``` cd maxomod ``` ### Data Preparation Human sequencing data: [EGAS00001007318](https://ega-archive.org/datasets/) [due to patient data, access is restricted] Mouse sequencing data: [GSE234246](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE234246) Proteomics data: [PXD043300](https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD043300) Phosphoproteomics data: [PXD043297](https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD043297) ### Organize Data All data should be organized in datasets using the following structures ``` datasets/ consortium/ / 01_received_data/ / cohort/ ``` The pipeline expects `fastq.gz` files for the sequencing data, `txt` files for the proteomics data and `csv` files for the phosphoproteomics data. Please, use DVC to see, which exact file names are required: ```bash dvc status srna_organize_samples proteomics_organize_samples phosphoproteomics_organize_samples rnaseq_nextflow ``` #### Automatic download (optional) To automatically download the RNAseq & miRNAseq data we provide a download script, which can be executed using the following commands: ```bash dvc unfreeze sra_prefetch sra_fastq_dump sra_organize dvc repro ``` ## Reproducing Results To reproduce the analysis results, execute the following command: ```bash dvc repro ``` This command will run the predefined pipelines to process and analyze the data according to the methodology described in the associated publication. All steps will be executed in a docker container automatically using the `docker_wrapper.sh` script. All docker images will be automatically downloaded and are available in the [Packages section](https://github.com/orgs/imsb-uke/packages?repo_name=MAXOMOD_Pipeline) on GitHub. ## Contributing We welcome contributions to enhance the reproducibility and scope of the analysis. ## Collaboration For questions or collaboration offers, please contact the project's principal investigators via email provided on the MAXOMOD project page: [MAXOMOD Contact Information](https://www.gesundheitsforschung-bmbf.de/de/maxomod-multi-omische-analyse-axono-synaptischer-degeneration-bei-motoneuronerkrankungen-9409.php).