Moore Notes 9 24 14
From OpenWetWareJump to navigationJump to search
- Participants: Katie, Tom, Stacia, Stephen, Dongying, Guillaume, Sarah, Josh, Patrick, Ladan
- Interesting papers:
- SAR11 marine diversity patterns validate our predictions (cites our ISME paper)
- Talks about seasonal diversity as an "emerging paradigm"
- Stephen: has a tool https://github.com/snayfach/SRAtools
- to download and process data from NCBI SRA
- converts file types
- Tom: half way through shotmap draft
- Next to Stephen
- Sarah: Comparing taxonomic and functional diversity in metagenomic samples (slides)
- Compare gene families of interest to 37 taxonomically informative "elite" families
- For each pair of samples, compute KR "earth mover's" distance for each family
- Then look at KR for families of interest vs. KR distributions for elite families
- What is KR measuring exactly? Does it depend on number of sequences and their abundances?
- How many samples and how diverse do they need to be? Within vs. between sample diversity? Inter-study variation a problem?
- Positive controls? Nitrite reduction, glycoside hydrolases
- How to summarize over all pairwise comparisons? Multiple testing?
- Alternative distance measures
- Future calls
- Mondays @ 1:30pm starting 10/6
- Oct 6: tentative shot map call
- Oct 13: TBD
- Oct 20: Josh will present on beta diversity and range shapes