aleixop/metat_bacterivory

Code used for data processing and analyses in "Gene expression dynamics of natural assemblages of heterotrophic flagellates during bacterivory"

Gene expression dynamics of natural assemblages of heterotrophic flagellates during bacterivory

This repository contains code and data included in:

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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

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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.