From 34eded4e94e750674d8b879918a9590d5ef82353 Mon Sep 17 00:00:00 2001 From: Simeon <51403284+simeross@users.noreply.github.com> Date: Mon, 23 Dec 2024 15:23:54 +0100 Subject: [PATCH] update README --- README.md | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index aabb05d..8c19cb8 100644 --- a/README.md +++ b/README.md @@ -7,15 +7,18 @@ This repository contains the supplementary code and intermediary data for the me The repository includes the following contents: -1. **Code**: - - `metabarcoding_analysis.R`: R script for the metabarcoding data analysis, including data preprocessing, diversity analysis, and statistical testing. - - `metabarcoding_functions.R`: Custom functions used in the metabarcoding data analysis. +1. **'analysis' folder**: contains scripts and intermediary files used and generated in the analysis. +Analysis was largely conducted per primer used in metabarcoding and then synthesized in some higher level analyses. +For each primer pair, the following is provided + - R script for the metabarcoding data analysis, including data preprocessing, diversity analysis, and statistical testing. + - Intermediary metabarcoding data, including amplicon sequence variants (ASVs), taxonomy, ASV counts for each sample and DADA2 processing logs. + - Metadata for the samples, including NDVI, and other relevant variables. -2. **Data**: - - `raw_metabarcoding_data.csv`: Raw metabarcoding data, including OTU (Operational Taxonomic Unit) counts for each sample. - - `metadata.csv`: Metadata for the samples, including information such as field location, plant growth status, and other relevant variables. +2. **'manuscript files' folder**: contains the larger tables presented in the manuscript -3. **README.md**: This file, providing an overview of the repository and instructions for use. +3. **'SRA submission' folder**: contains metadata used for submission of reads to NCBI's Short Read Archive + +4. **README.md**: This file, providing an overview of the repository and instructions for use. ## Usage @@ -27,7 +30,7 @@ The repository includes the following contents: 2. Ensure you have the necessary R packages installed. All necessary dependencies required by the analysis scripts are listed in the top chunks of the respective scripts. -3. Obtain the raw read data from [ENA](LINK-MISSING) +3. Obtain the raw read data from [SRA](https://www.ncbi.nlm.nih.gov/bioproject/) under the BioProject with the accession PRJNA1191665. 4. Open the R Markdown file and run the code to reproduce the metabarcoding data analysis. @@ -39,7 +42,7 @@ If you use the code or data from this repository in your own work, please cite t To be updated upon publication ``` -Additionally, please acknowledge the use of this supplementary repository by citing it as follows: +Before publication, please acknowledge the use of this supplementary repository by citing it as follows: ``` MP Tangvik et al. (2024). Supplementary code and data for 'Drone imagery and metabarcoding as diagnostic tools of poor growth in potato fields' [Data set]. GitLab. https://gitlab.nibio.no/simeon/persdatter-et-al-2025-metabarcoding -- GitLab