• Purpose of this repository
• Workflow examples
  • Transcription factors
    • Execution
    • Dependencies
  • Histone marks
    • Execution
    • Dependencies
  • RNA-seq (TODO)
• Data organisation
• Documentation
• Contact

This git repository holds shared code for the analysis of Next Generation Sequencing data related to gene regulation: ChIP-seq, RNA-seq, and related technologies.

The goals are multiple.

1. Avoid duplication of efforts by sharing the developments of different bioinformaticians involved in ChIP-seq and RNA-seq projects.

2. Ensure portability and re-usability of the code.

3. Enable validation of the code by independent users.

This repository contains basic workflow examples.

Pre-requisites:

• R 3+
• Python 3.3+
• Snakemake 3.3+

See doc/install_protocols/install_snakemake_workflows.Rmd for a detailed manual on how to install programs and dependencies.

The file factor_workflow.py is designed to perform ChIP-seq analysis on transcription factor studies.

Two associated config files are designed to work with this workflow: Athaliana-Myb.yml and Scerevisiae-GCN4.yml.

In order to launch the workflows, you can enter the following commands from the root of the repository:

snakemake -s scripts/snakefiles/workflows/factor_workflow.py --configfile examples/Scerevisiae-GCN4/Scerevisiae-GCN4.yml -p -n
snakemake -s scripts/snakefiles/workflows/factor_workflow.py --configfile examples/Athaliana-Myb/Athaliana-Myb.yml -p -n

This ensures the workflows are executable. Remove the -n option to actually run them.

• SRA Toolkit
• Bowtie 2
• SAMtools
• FastQC
• bedtools
• HOMER
• MACS1.4
• MACS2
• SWEMBL
• RSAT

This workflow is adapted for histone marks that show larger profiles than usual TF marks.

The file histone_workflow.py is designed to perform ChIP-seq analysis on histone marks data.

Two associated config files are designed to work with this workflow: Celegans-H3K4me3.yml and Celegans-H3K27me3.yml.

In order to launch the workflows, you can enter the following commands from the root of the repository:

snakemake -s scripts/snakefiles/workflows/histone_workflow.py --configfile examples/Celegans-H3K4me3/Celegans-H3K4me3.yml -p -n
snakemake -s scripts/snakefiles/workflows/histone_workflow.py --configfile examples/Celegans-H3K27me3/Celegans-H3K27me3.yml -p -n

This ensures the workflows are executable. Remove the -n option to actually run them.

• SRA Toolkit
• Sickle
• BWA
• SAMtools
• FastQC
• bedtools
• HOMER
• MACS1.4
• MACS2
• SWEMBL

From the example config files, it is assumed that, in order to run the workflows, you have the following file organisation:

/data/
    Athaliana-Myb/
        GSM1482283/
            SRR1554463.sra
        GSM1482284/
            SRR1554464.sra
        design.tab
        samples.tab
    Celegans-H3K27me3/
        GSM1217457/
            SRR1198569.sra
        GSM121745/
            SRR1198570.sra
        GSM121745/
            SRR1198571.sra
        GSM1217460/
            SRR1198572.sra
        design.tab
        samples.tab
    Celegans-H3K4me3/
        GSM120836/
            SRR952381.sra
        GSM1217457/
            SRR1198569.sra
        design.tab
        samples.tab
    Scerevisiae-GCN4/
        GSM147015/
            SRR1542426.sra
        GSM1470160/
            SRR1542427.sra
        GSM147016/
            SRR1542428.sra
        GSM147016/
            SRR1542429.sra
        GSM1470163/
            SRR1542430.sra
        GSM1470164/
            SRR1542431.sra
        design.tab
        samples.tab
    genomes/
        ce10/
            ce10.fa
        sacCer3/
            sacCer3.fa
        TAIR10/
            TAIR10.fa

All the data is available from the GEO platform. samples.tab and design.tab can be found in the repository examples section.

More documentation can be found in the doc directory. (under construction)

It includes:

• Instructions for the installation of dependencies (to be refhreshed)
• RSAT install guide (to be refreshed)
• Instructions for building a virtual machine on the IFB cloud or under VirtualBox
• Some wiki material

• Claire Rioualen [email protected]
• Jacques van Helden [email protected]