primer effects before/after introduction of new primers
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Description
New primers were introduced gradually in 2015. Here's what's different:
- Barcodes are now located on the forward (515) primer to enable the usage of various reverse primer constructs to enable longer amplicons (tested on 806r and 926r).
- Degeneracy was added to both the forward and reverse primers (see below), with the intent of removing known biases against Crenarchaeota/Thaumarchaeota (515f modification) and the marine and freshwater Alphaproteobacterial clade SAR11 (806r modification).
The hope is that these new primers improve detection of certain groups. But this complicates comparison of community composition before and after the new primers were introduced. _We need to make sure that the conclusions we draw from large meta-analyses are not due to primer differences alone._
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Research direction
No files, tests, or entry points are named. Start by locating the analyses and datasets that compare community composition before and after the 2015 primer changes; done means assessing whether primer differences alone explain conclusions in the large meta-analyses.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100