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How to Use VAMPS



  • Introduction

  • Community Visualization - Heatmap Comparison

  • Community Visualization - Taxonomy Tables

  • Exporting Taxonomic Counts

  • Exporting Clustering and Diversity Data

  • Exporting Fasta Sequences

  • Clustering and Diversity

    Downloading the Rarefaction data package

    Select your project from the drop-down menu and click continue.

    diversity

    Right-click on the link to download your file. Due to the size of the rarefaction and cluster data files, the files are compressed and will need to be unzipped.

    rarefaction

    The rarefaction files are packaged by project. The rarefaction package includes the following files:

    • The .ace file contains ACE values.
    • The .chao contains Chao values.
    • The .rarefaction file contains resampling of OTUs for creation of rarefaction curves.

    To create a rarefaction curve, import one .rarefaction file into Excel, using the Excel default import parameters. Create a new X-Y chart using the numsequences column as the X-value. The unique 0.03, 0.06, or 0.10 columns can be used as Y-values.

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    Downloading the OTU Cluster data package

    Select your project from the drop-down menu and click the OTU Cluster Files radio button. Click continue.

    otus

    The output files are compressed and will need to be unzipped.

    • The .fa file is a fasta file of the unique sequences used to create the clusters.
    • The .names is a text file specifying the additional tags that have the exact same sequence.
    • The .list file specifies the OTU membership - one line for each OTU width.
      The first item in this file is the OTU width (unique or 0.01-0.10 corresponding to 0-10%), the second is the number of OTUs, and following this is the list of OTUs. Commas separate tags within the same OTUs and tabs separate one OTU from the next.
    • The .otu file specifies the OTU sizes - one line for each OTU width.
      The first item in this file is the OTU width (unique or 0.01-0.10 corresponding to 0-10%), the second is the number of OTUs, and following is the list of OTU sizes separated by tabs.
    • The .tax shows the taxonomy file corresponding to the .list file - one line for each of the the otu widths 0.03, 0.06, and 0.10.
      Clusters are tab separated, and within each cluster are the lists of taxa and their counts in descending order, separated by commas.

    NOTE: The .list file and the .otu file may exceed Excel limitations on cell size and number of columns. Other software may be required to utilize these data.


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