/remap-pipeline

As the ReMap project expands dramatically and regulatory catalogs for other species are requested, it becomes essential to enable joint efforts between the ReMap team and external teams. This is essential for future collaborative production efforts. Briefly, our pipelines uses SnakeMake either in a Conda or Singularity environment depending on the HPC resources, where Torque and Slurm managers are both supported

Primary LanguagePython

remap-pipeline

Description

ReMap is a project which goal is to provide a catalogue of high-quality regulatory regions resulting from a large-scale integrative analysis of hundreds of transcription factors and general components of the transcriptional machinery from DNA-binding experiments. This git contain all the workflow necessary to run an analysis ReMap style from sample annotation files to the a final BED catalogue.

Installation

Requirements

  • Python 3
  • Snakemake >= 5.5.1
  • Recommended : Conda/Docker/Singularity

Step by step

  1. Pull the git
  2. That's all

Usage

Please follow the wiki page for step by step inforamtions.

General

  1. Prepare the metadata from your annotation file by extracting downloading info (See README.md in 1.metadata/)
  2. Create cluster config and snakemake config to match your set up (See example in 2.scripts/cluster_configuration)
  3. Get necessary files such as reference genome (See README.md in 3.genome/)
  4. Create a launch bash script (See example in root directory)
  5. Run launch script

Folder organisation

The worklow (see wiki) will create the necessary folders for most of the main processing steps.

Folder in bold will be created by the workflow.

  • 1.metadata/
  • 2.scripts/
  • 3.genome/
  • 4.preprocessing/
    • log/
    • raw_bam/
    • raw_fastq/
    • rm_mismatch_bam/
    • sam/
    • sort_bam/
    • trim_fastq/
  • 5.bam/
  • 6.peakcalling/
  • 8.quality/
  • 9.bed/

Compute clusters specificities

remap-pipeline can be run with Conda or Docker/Singularity and Torque and Slurm.

Examples are in launch scipts.

Contributing

License

Under GNU GPLv3 licence.

References

ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments Jeanne Chèneby, Zacharie Ménétrier, Martin Mestdagh, Thomas Rosnet, Allyssa Douida, Wassim Rhalloussi, Aurélie Bergon, Fabrice Lopez, Benoit Ballester. Nucleic Acids Research, 29 October 2019, https://doi.org/10.1093/nar/gkz945