Code for the paper:
S. L. Tsola, Y. Zhu, Y. Chen, I. A. Sanders, C. K. Economou, V. Brüchert, Ö. Eyice (2023). Methanolobus use unspecific methyltransferases to produce methane from dimethylsulfide.
This repo contains the code for analysing the amplicon data presented in the paper using QIIME2 as well as code for creating a custom mcrA database. Furthermore, it has R scripts detailing the bioinformatic analysis of the amplicon data and how the various graphs were made using ggplot2. Lastly, program usage information is given for PAST (used for the Spearman correlation analysis).
Any help with improving the scripts or any other comments are greatly appreciated.
- mcrAseq_analysis-QIIME2.sh - Script for the qiime2 analysis of mcrA sequences from the Baltic Sea samples
- mcrA_sample-metadata.tsv - Metadata file of Baltic Sea mcrA samples
- mcrA_analysis-microeco.R - Script for microeco mcrA analysis
- mcrAseq_Database - Script for creating the mcrA database
- Graphs_AverageGas_Depth_qPCR_heatmaps-ggplot2.R - Script containing information on the creation of all R graphs (avg gases, metag/T heatmap, qPCR)
- Spearman_correlation-PAST.txt - Step-by-step guide to using PAST for the Spearman's correlation analysis
- Baltic_mcrA_PCoA_scores.csv - csv file imported into PAST
- LICENSE.md
This project is licensed under the terms of the MIT License. See the LICENSE.md for further information.