MCScanX_Assistant

Overview

This repository stored the custom codes we used for the re-analysis of the protocol from Wang et al. Nature Protocols https://doi.org/10.1038/s41596-024-00968-2 (2024).

It is intended to provide researchers with access to reproduce our work, facilitating future researchers to easily prepare the input data and install of MCScanX tool.

Usage

Refer to Usage documents for details.

Note

If you are new to Snakmake, please refer to this page on how to set-up SnakeMake. Make sure to test the example data below before running the workflow on your data.

# Test if you have successfully installed the SnakeMake
mamba activate snakemake
snakemake --help

Note

Begin with a config.yaml file as below (detailed the input files requested).

The six species of NCBI assemblies are used in this analysis, including B. carinata, A. suecica, A. arenosa, T. arvense, A. thaliana, B. oleracea.

Arguments

config.yaml

species_name:
  - Athaliana

ncbi_genomes:
    Athaliana:
        ncbi_assembly: "data/ncbi_download/GCF_000001735.4.zip"
        assembly_id: "GCF_000001735.4"
        feature_table: "data/ncbi_download/GCF_000001735.4_TAIR10.1_feature_table.txt.gz"
        species: Athaliana

Note

Optional: To download extra ncbi assembly 'XX.zip' from NCBI, users can substitue the ncbi_assembly id (e.g., GCF_000001735.4) with yours in the command below:

curl -OJX GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_000001735.4/download?include_annotation_type=GENOME_FASTA,GENOME_GFF,RNA_FASTA,CDS_FASTA,PROT_FASTA,SEQUENCE_REPORT&filename=GCF_000001735.4.zip"

Running

Now, you can run the pipeline using the following commands:

# Download the package
git clone https://github.com/zx0223winner/MCScanX_Assistant.git

# enter the working directory
cd MCScanX_Assistant

Note

Due to the size of sample files (we have prepared users with the standard input files of NCBI genome assemblies for the six species of NCBI assemblies are used in this analysis, including B. carinata, A. suecica, A. arenosa, T. arvense, A. thaliana, B. oleracea. ).

please download the test data - MCScanX_Assistant_data.tar.gz through the Google drive link

(optional) please download the test result - MCScanX_Assistant_results.tar.gz through the Google drive link. This file includes complete running results for users to check.

# Then decompress the file MCScanX_Assistant_data.tar.gz under the MCScanX_Assistant directory,
# This will bring you a data folder with test files ready 
tar -xvzf MCScanX_Assistant_results.tar.gz

# Then you can give a dry run by the following command.
snakemake --use-conda --cores all -s workflow/Snakefile_Input_preparing -n

# If everthing is OK, then you can test the pipeline by running one after another:
snakemake --use-conda --cores all -s workflow/Snakefile_Input_preparing
snakemake --use-conda --cores all -s workflow/Snakefile_Ks_distribution_plot
snakemake --use-conda --cores all -s workflow/Snakefile_MCScanX_6species

License

The code within this repository is licensed under the MIT License. Please refer to the license file for more information on the terms and conditions of using and contributing to this project.

Ciation

If you used the codes in this respository, please cite the link.

Declaration of generative AI and AI-assisted technologies

GitHub tool logo generation. Author reviewed and edited the content as needed and takes full responsibility for the content.