hollygene CornellPostdoc issues

hollygene / CornellPostdoc

Various scripts I used during my tenure as a Postdoctoral Associate at Cornell University

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Analyze sequences from 6/27/21 run

#16 hollygene opened 3 years ago
0
Are any of our AMR genes located on plasmids?

#15 hollygene opened 3 years ago
0
Another thing for us to know: how many of these isolates in dogs are multidrug resistant? And which genes are correlated with multidrug resistance – which I guess, would be genes that we see as correlated with resistance to more than one antibiotic; we need to summarize that somehow.

#14 hollygene closed 7 months ago
2
Analyze sequences from iSeq run 5/15/21 and 5/24/21

#13 hollygene opened 3 years ago
1
Cross-reference our AMR genes with other AMR databases/AMR gene finding algorithms

#12 hollygene opened 3 years ago
1
SNP calling

#11 hollygene opened 3 years ago
15
Need to find what genes the significantly associated SNPs from treeWAS reside in

#10 hollygene opened 3 years ago
0
Microbial GWAS - want to correlate resistance phenotypes with genotypes/SNPs/other mutations

#9 hollygene opened 3 years ago
22
Has anyone looked at the isolates whose phenotype and genotype don't match?

#8 hollygene opened 3 years ago
1
Backtrack from SNP to genes

#7 hollygene opened 3 years ago
0
Reading up to date relevant literature

#6 hollygene opened 3 years ago
1
Compare SNP callers

#5 hollygene opened 3 years ago
4
Run AMRFinder on BioProjects

#4 hollygene opened 3 years ago
1
Run treeWAS

#3 hollygene opened 3 years ago
13
Correlate phenotype and genotype - compare AMR gene classes with resistance phenotypes from Olga's spreadsheets

#2 hollygene opened 3 years ago
3
Correlate phenotype and genotype - compare AMR gene classes with resistance phenotypes from Olga's spreadsheets

#1 hollygene opened 3 years ago
0