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00a_Metadata.md

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Tutorial followed: https://bioinformaticsworkbook.org/dataAnalysis/Metagenomics/Qiime2.html

Dataset from this paper: Castrillo, G., Teixeira, P.J.P.L., Paredes, S.H., Law, T.F., de Lorenzo, L., Feltcher, M.E., Finkel, O.M., Breakfield, N.W., Mieczkowski, P., Jones, C.D., Paz-Ares, J., Dangl, J.L., 2017. Root microbiota drive direct integration of phosphate stress and immunity. Nature 543, 513–518. doi:10.1038/nature21417

Input data

Input folder contains input files list # list used to download reads data manifest.csv # manifest file AllMetadata.tsv # File containing all metadata

Output data

Visualizations folder contains all visualization files:

  • Summary Statistics/Taxa bar plot

    • demux.qzv
    • table-dada2.qzv
    • table-with-metadata-dada2.qzv
    • taxonomy.qzv
    • taxa-bar-plots.qzv
    • taxa-bar-plots-filtered.qzv

  • PCA type plots

    • bray_curtis_emperor.qzv
    • jaccard_emperor.qzv
    • pcoa-visualization.qzv
    • heatmap.qzv