Metagenomics Tutorial (Long Running) Answers

These are the answers to the questions from the Metagenomics Tutorial

Taxonomic section:

1. 30
2. 10
3. 200,000/sample
4. MetaPhlAn version 2.1.0 (28 April 2015)
5. s__Neisseria_unclassified 7.76249
6. SRS015044: p__Actinobacteria & SRS015893: p_Firmicutes
7. Phylum Candidatus_Saccharibacteria, Present only in sample SRS015044
8. SRS015044 supragingival plaque
9. metaphlan_out
10. Yes, there is separation between the tongue samples and the plaque samples but there appears to be no separation between subgingival and supragingival. The separation occurs along PC1.

Functional section:

1. SRS015893
2. No
3. 246 (KOs different across body sites)
4. 16 (KEGG Pathways different across body sites)
5. ko00281: Geraniol degradation . corrected p-value: 5.19e-6
6. 22
7. Higher in the tongue samples.
8. Should look like this: