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Metagenomics Tutorial (Long Running) Answers
Gavin Douglas edited this page Apr 10, 2017
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1 revision
These are the answers to the questions from the Metagenomics Tutorial
Taxonomic section:
- 30
- 10
- 200,000/sample
- MetaPhlAn version 2.1.0 (28 April 2015)
- s__Neisseria_unclassified 7.76249
- SRS015044: p__Actinobacteria & SRS015893: p_Firmicutes
- Phylum Candidatus_Saccharibacteria, Present only in sample SRS015044
- SRS015044 supragingival plaque
- metaphlan_out
- 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:
- SRS015893
- No
- 246 (KOs different across body sites)
- 16 (KEGG Pathways different across body sites)
- ko00281: Geraniol degradation . corrected p-value: 5.19e-6
- 22
- Higher in the tongue samples.
- Should look like this:
- Please feel free to post a question on the Microbiome Helper google group if you have any issues.
- General comments or inquires about Microbiome Helper can be sent to [email protected].
Useful Links
Main SOPs
Amplicon SOP v2 (virtual box workflow)
Amplicon SOP v2 (qiime2-2022.11)
Amplicon SOP v2 (qiime2-2024.5)
PacBio Amplicon SOP v2 (qiime2-2022.2)
Tutorials
- CBW 2024 Workshops
- CBW-IMPACTT-workshop-tutorials-2023
- Intro to Unix
- ICG workshop tutorials 2023
- IMPACTT workshop tutorials 2022
- PICRUSt2 (CBW 2021)
- Metagenomics (CBW 2021)
- Intro to GNU Parallel
- BIOC4010 16S Tutorial
- Metagenomics Tutorial (Humann2 based)
- Download From SRA
- Random Forest Tutorial in R
- Other Tutorials