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Week 6 tests
Nelly-Wambui edited this page Jan 27, 2022
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Objectives:
- Visualizing functional analysis using STAMP
- Report writing
- Running Yosef's pipeline
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For functional analysis visualization, we used Statistical Analysis of Metagenomic Profiles (STAMP)
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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:
- conda create -n stamp python=2.7
- conda activate stamp
- pip install numpy
- pip install cython
- pip install biom-format==2.1.7
- pip install STAMP
- conda install -n stamp -c asmeurer pyqt=4
- STAMP
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We then uploaded the metadata and the pathway picrust results which we visualized in the variety of plots in STAMP
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This tutorial video helped us in understanding what STAMP entails in addition to the guidance we received
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The colors represent group fields
- Extended error bar plots show what members are contributing to the community
- Heat map plots show abundance of the composition of the communities
- Bar plots and Box plots can be used to indicate specific microbiome essential in a community or in this case a pathway of interest
- PCA plots show any significant patterns or trends that can relate a community to ecology and diversity
- We continued with our report writing and managed to add some more details to it.
- The progress can be seen here