Moore Notes 7 10 13
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Group Call
- Participants: Katie, Stephen, Tom, Josh, Ladan, Dongying
- Dongying: wants to do metagenomic simulations for TreeOTU validation
- Wants to simulate a community
- Reads need to be >200bp
- Stephen has simulation pipeline using Grinder with communities pre-defined
- Also need to calculate 16S copy number (try Steve Kembel's tree based inference of this)
- Josh: talked to Jack Gilbert about samples
- Has a call scheduled with him next week (Monday 10am)
- Jack will put people with samples on call
- Josh will follow up with Jonathan
- ncRNA gene families
- Could scan English Channel unmapped reads in similar manner to HOT/ALOHA ncRNA paper: http://www.ncbi.nlm.nih.gov/pubmed/19444216
- Stephen: could be hard to build de novo families from short reads
- Try assembly
- Tom: might work because English Channel and HOT/ALOHA are 454 length reads
- How hard is it to build a model?
- Structure based alignment is challenging
- SCFGs are slow
- Another sifting step would be to run them against vFams for viruses
- Stephen: been playing with metagenomic gene finders as an alternative to 6-frame translation
- Reduce the volume of data to search in MRC six-fold
- 5% reduction in sensitivity
- Not clear yet if the filtered ones are biased or effect relative abundance estimates
- Used fragGeneScan
