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

Day 2 Afternoon #51

Open
alipirani88 opened this issue Feb 14, 2019 · 1 comment
Open

Day 2 Afternoon #51

alipirani88 opened this issue Feb 14, 2019 · 1 comment
Labels
data enhancement

Comments

@alipirani88
Copy link
Owner

No description provided.

@alipirani88
Copy link
Owner Author

alipirani88 commented Feb 14, 2019 •
edited
Loading

  • - Choose K. pneumo genomes for BLAST, ARIBA & MLST (ZENA) Holt et al. (2015) PNAS, Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health.
  • - Assemble the K. pneumo genomes
  • - Make a metadata file by subsetting the supplement file (ZENA)
  • - Change to pheatmap (plot AMR genes with origin) (ZENA)
  • - Explore Ariba all report: (Zena)
  • - Add exercise to run MLST and overlay on heatmap (ZENA)
  • - Decide what genome comparison to do for A. baumanii (Evan)
  • - Fraction of genomes that are putative phage?
  • - What genes are in genomic rearrangements?
  • - Add solution section to the questions asked.
  • - Change the Blast exercise to finding KPC gene from KPC dataset.
  • - Ask to run Ariba MLST step on 5-6 samples. Time this exercise.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
data enhancement
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@alipirani88