Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Optimize VSEARCH parameters #41

Open
lina-kim opened this issue Oct 19, 2022 · 0 comments
Open

Optimize VSEARCH parameters #41

lina-kim opened this issue Oct 19, 2022 · 0 comments
Labels
analysis-needed Less implementation, more analysis nice to have Stretch goal if time

Comments

@lina-kim
Copy link
Collaborator

Cross-reference low VSEARCH hits from ECAM and MSK datasets?

  • Host 16S? Contamination? mt16S in diet? Index hopping?
  • Nick: “85% [identity] is quite low for a gut cohort”
  • Use consensus or confidence threshold? Weight by confidence in a given type?
@lina-kim lina-kim added nice to have Stretch goal if time analysis-needed Less implementation, more analysis labels Jan 30, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
analysis-needed Less implementation, more analysis nice to have Stretch goal if time
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@lina-kim