biocore / biocore/emp

primer effects before/after introduction of new primers

Open
#45 6 comments 0 reactions 0 assignees View on GitHub
analysis
Dominant language
Jupyter Notebook
Stars
169
Forks
68
PR merge metrics
No merged PRs in 30d

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._

Contributor guide

No contributing guide indexed for this repository

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

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.