1. bioBakery
  2. Untitled Project
  3. biobakery

Wiki

Clone wiki

biobakery / micropita

microPITA Tutorial

microPITA (microbiomes: Picking Interesting Taxonomic Abundance) is a computational tool enabling sample selection in two-stage (tiered) studies. Using two-stage designs can more efficiently allocate resources, reducing study costs, and maximizing the use of samples.

microPITA is available as a Galaxy module, as well as a bitbucket repository. For additional information, please refer to the microPITA paper.

We provide support for microPITA users. Please join our Google group designated specifically for microPITA users. Feel free to post any questions on the google group by posting directly or emailing micropita-users@googlegroups.com.



Overview

The following figure shows the workflow for microPITA.

microPITA.png

1. microPITA (Galaxy module)

microPITA requires a PCL or BIOM input file. For further information on details of format, please refer to the documentation. For the purpose of this tutorial we will be using a sample input file depicting the general format of the input file.

  • Go to the Huttenhower Galaxy server.
  • Click on the microPITA link on the left pane, and then on the Load data for microPITA link.
  • Click on the Choose File button to select the input file OR enter the URL in the URL/Text text box to upload the data. Click on the Execute button.
micropita_step1.png
  • Click on the Run microPITA link on the left pane.
    • Select the input data from the Input file drop-down menu.
    • Specify the last metadata row in the sample, after which the microbial species are listed (this is Weight in our sample dataset). For this demo, select Label
    • Select the sample selection method from the Select method drop-down menu. For this demo, select representative.
    • Click on Execute
micropita_Step2.png

The results will appear on the right pane. You may proceed with viewing it (by clicking on the Eye symbol) or downloading it on your computer (by clicking on the Save symbol). The output file will depict the samples that are representative of the survey.


2. microPITA (Bitbucket repository)

microPITA may also be downloaded as a bitbucket repository. For instructions on installation, dependencies and further details please refer to the microPITA documentation.

  • Open a terminal, and change the directory to that of microPITA.
  • Place the sample input file in the input folder, and run the following command:
$ python MicroPITA.py --lastmeta Label -m representative input/Test.pcl output.txt

This will generate an output.txt file containing the results.

For further analysis options and more information, please refer to the detailed documentation.


Notes

Please visit http://huttenhower.sph.harvard.edu/micropita for more information

Updated