Transcriptome-Microbiome Integration

This Nextflow pipeline automates the integration of transcriptomic expression profiles and microbiome abundance data (OTU tables), performing cross-correlation analysis to uncover potential associations between host transcriptome-microbiome associations.

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prerequisites

This pipeline requires Nextflow 25.04.2 or higher.

Follow this tutorial to install Nextflow.

We use Conda to avoid dependency conflicts and ensure reproducible environments across different systems.
Make sure you have installed Conda 25.5.1 or higher.

Follow this tutorial to install Miniconda, a miniature version of Anaconda.

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installing

Clone this repository:

git clone https://github.com/SantosRAC/transcriptome_microbiome_integration.git
cd transcriptome_microbiome_integration

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input files

This pipeline requires an input sample containing the following information:

• Expression Matrix: A TSV file containing RNA expression from the transcriptome
• OTU Table: A TSV file containing the OTU information of the microbiome

See an example of input files here.

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configuring

After installing, make sure to update the configuration file with your input file paths.

See an example below:

head -n13 config/nextflow.config

params {
  // $publishDir relative paths
  out_dir         = "../results"
  report_dir      = "report"
  environment_dir = "../envs"
  conda_cache_dir = "conda-cache"

  // path to samples
  day_file          = "$projectDir/../samples/filtered_otu_table_day_filtered_rel_abund_cv_filtered.tsv"
  night_file        = "$projectDir/../samples/filtered_otu_table_night_filtered_rel_abund_cv_filtered.tsv"
  expression_matrix = "$projectDir/../samples/expression_matrix.tsv"

Tip

This is the configuration file used in this study.

running the pipeline

From the pipeline root directory, execute:

cd transcriptome_microbiome_integration

# example for running the pipeline locally  
nextflow run workflows/main.nf -c config/nextflow.config -profile local

# you can use the -resume flag to re-run the pipeline if some step failed
nextflow run workflows/main.nf -c config/nextflow.config -resume -profile local

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questions?

For suggestions, bug reports, or collaboration, feel free to open an issue.