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Working group bacterial genomics, part 3

  1. annotate all the assemblies with prokka and cluster the genes in groups of orthologs using roary

with -i flag in roary you can decide the minimum percentage identity for blastp (default 95%); do you think this value is appropriate for your dataset?

Note: since your dateset is very small for performing GWAS, you will select a set of few accessory genes to be used in the final part of the course

  1. from gene_presence_absence.csv produced by roary select three accessory genes, present in a significant number of samples (e.g. 1/3 of your dataset)
  2. add to the tab-separated values (TSV) file produced during working with your data part 2 session 2 three extra columns corresponding to the three selected genes, as follow:
FILE  ResistanceGenes Gene1 Gene2 Gene3
Samplename_1  GeneName-GeneName-...-GeneName  present absent  present
Samplename_2  ND  present absent  absent