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Week 6 tests

Nelly-Wambui edited this page Jan 27, 2022 · 1 revision

Objectives:

  • Visualizing functional analysis using STAMP
  • Report writing
  • Running Yosef's pipeline

Functional Analysis

  • For functional analysis visualization, we used Statistical Analysis of Metagenomic Profiles (STAMP)

  • We downloaded STAMP tool to be able to visualize the picrust results (functional analysis results) obtained after running the nf-core/ampliseq pipeline using the stingless bee data

  • The following steps were followed for downloading and opening the GUI STAMP from the terminal:

    1. conda create -n stamp python=2.7
    2. conda activate stamp
    3. pip install numpy
    4. pip install cython
    5. pip install biom-format==2.1.7
    6. pip install STAMP
    7. conda install -n stamp -c asmeurer pyqt=4
    8. STAMP
  • We then uploaded the metadata and the pathway picrust results which we visualized in the variety of plots in STAMP

  • This tutorial video helped us in understanding what STAMP entails in addition to the guidance we received

  • The colors represent group fields

STAMP Plots

  • Extended error bar plots show what members are contributing to the community
  • Heat map plots show abundance of the composition of the communities

Bar plot for specific pathway

  • Bar plots and Box plots can be used to indicate specific microbiome essential in a community or in this case a pathway of interest

Box plot

PCA plot

  • PCA plots show any significant patterns or trends that can relate a community to ecology and diversity

Report Writing

  • We continued with our report writing and managed to add some more details to it.
  • The progress can be seen here
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