Gene expression dynamics of natural assemblages of heterotrophic flagellates during bacterivory

This repository contains code and data included in:

Obiol, A., López-Escardó, D., Salomaki, E.D, Wiśniewska, M.M., Forn, I., Sà, E., Vaqué, D., Kolísko, M., and Massana, R. Gene expression dynamics of natural assemblages of heterotrophic flagellates during bacterivory. Microbiome 2023; 11: 134. doi: 10.1186/s40168-023-01571-5

How to use this code

1. Clone this repository

Download all scripts by using:

git clone https://github.com/aleixop/metaT_bacterivory.git

2. Download the data

Data used in all the analyses are available at FigShare. Download the zip file there and copy the obtained data/ directory to the root of the project you just created in the previous step.

3. Run the code

A separate R Markdown file is available for each figure/table present in the paper.

Raw data

Raw data used for this project is available at ENA with accession numbers PRJNA973582 and PRJNA543770. You can find the correspondence between NCBI/ENA accession numbers and real sample names and the rest of metadata in the full_metadata.txt file.