IFN646 - Portfolio item 4
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IFN646 - Portfolio item 4
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Overview For this portfolio item, you will focus on differential microbial abundance. You will need to download some datasets, develop some code, and upload your analysis to Blackboard. We strongly recommend using a Jupyter Notebook and submitting an HTML export. |
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1. Data for the portfolio item You are provided with three files:
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2. Tasks
Overall goal
The overall goal of the analysis is to understand how smoking impacts the nose and throat microbiomes.
You will perform your analysis using Calour, as we have done in class. Note that for some questions, you may need to write some additional code to process the results.
Task 1 [1.75 marks]
Identify which bacteria have a differential abundance between the nose and throat (irrespective of the smoking status). [1.5 marks]
Try to report names rather than simply the ID of the OTUs. [0.25 mark]
Note that the taxonomy data is hierarchical. For each line, you get:
the ID
the kingdom, with prefix k__
the phylum, with prefix p__
the class, with prefix c__
the order, with prefix o__
the family, with prefix f__
the genus, with prefix g__
the species, with prefix s__
If genus and species are available, you should give both. For instance, for ID 1097955 , you should report Staphylococcus aureus . Note that we remove the prefixes.
If the species is not available, give the genus only. For instance, for ID 242061 , you should report Catellatospora .
If both the genus and species are unavailable, report the most informative level. For instance, Gaiellaceae for 104172 , or Chloroplast for 47632 .
Task 2 [1.75 marks]
Identify which bacteria have a differential abundance between smokers and non-smokers (irrespective of the sampling site). [1.5 marks]
Try to report names rather than simply the ID of the OTUs. [0.25 mark]
Task 3 [2.5 marks]
Identify which bacteria have a differential abundance in the nose between smokers and non- smokers. [1 mark]
Hint: look at the filter_samples() method in Calour.
Identify which bacteria have a differential abundance in the throat between smokers and non- smokers. [0.5 mark]
Are these results the same as those obtained in Task 2? Explain why. [0.75 mark] Try to report names rather than simply the ID of the OTUs. [0.25 mark]
3. Submission
You will submit your analysis through Blackboard, in the "Portfolio Item 4" folder.
We strongly recommend using a Jupyter Notebook, export your work as an HTML file, and upload this as your submission.
Alternatively, if you prefer not to use Jupyter, you can submit a PDF report that contains both your answers for each task and your Python code as appendix.
Submission will close at 11.59pm on the due date.
4. Academic honesty
This is an individual assessment, and you need to submit your own work. Standard plagiarism checks will be performed on your code. We also reserve the right to select some submissions and ask students to explain the reasoning behind their answers.
2022-10-08