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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

  • Export Taxonomic Counts

    Downloading the Taxonomic Counts Files

    Select the projects and custom datasets you are interested in. Each custom dataset contains a combination of datasets and will be treated as one. Select the output type. See the FAQ section for an explanation of how the datasets are normalized.



    Select the domain you are interested in. Click Get Taxonomy Data.



    Three output files will be generated. Depending on the size of the dataset, it may take a few seconds to download. Please allow time for all three files to finish. When ready, click the link for the desired output file and download.
    The three output files are:

    • TaxByTax - Reads having the same taxonomic assignment are grouped (coarsest grouping)
    • TaxByRefHVR - Reads with the best match to the same reference V6 are grouped (medium grouping)
    • TaxBySeq - Reads having the exact same sequence are grouped (finest grouping)




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    Saving Files in Different Browsers

    Instructions for saving a file are slightly different in the various browsers:

    • Mac OS X / Firefox. Right-click on the file name link and choose "Save Link As...".
    • Mac OS X / Opera. Right-click on the file name link and choose "Save Linked Content As...".
    • Mac OS X / Safari. Right-click on the file name link and choose "Save Linked File As...".
    • Windows / Firefox. Right-click on the file name link and choose "Save Link As...".
    • Windows / Internet Explorer. Right-click on the file name link and choose "Save Target As...".
    • Windows / Opera. Right-click on the file name link and choose "Save Linked Content As...".

    After exporting, the text files may be opened in a text editor. For Windows, the best text editor to use is Wordpad.


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    Importing Files to Excel Spreadsheets

    • In MS Excel for Windows, you can import a text file by selecting "Data/Import Data...".
    • In MS Excel for Mac, import a text file by selecting "Data/Get External Data/Import Text File..."
    • From the file dialog box, select the file you wish to import.
    • This brings up the Text Import Wizard. Follow steps 1 through 3:
      • Step 1 - Make sure "Delimited" is selected.
      • Step 2 - Make sure "Tab" is selected as the delimiter.
      • Step 3 - Click Finish.

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    Creating Skyline Plots

    Normalized data will be shown with decimals in the spreadsheet. You may find reading the spreadsheet easier by formatting the data to whole numbers.

    To plot the data, highlight all the dataset columns and click on the chart wizard. Select the 3-D column chart.



    The series axis (y-axis) shows the datasets, the category axis (x-axis) shows the otus, and the value axis (z-axis) shows the count.

    The chart can be rotated by clicking on a corner of the plot and dragging. The depth of the chart can be adjusted by clicking the plot, then go to the Format menu and choose Selected Data Series. Under the Options tab, you can adjust the chart depth.








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