LO - 2 - Getting data

[KatherineCaley]

• Published GenBank ID's (e.g. REFSOIL)
• Ensembl downloading and Installing

[GavinHuttley]

yapeng to help with the Duchene problem data after submitting

[KatherineCaley]

Genbank

Trying to get a published reference dataset with REFSOIL

• link to the publication (https://www.nature.com/articles/ismej2016168#Sec2)
• what we want:
  • genome sequences and their annotations. I’m assuming the motivation for why annotations are necessary will have been mainly covered by this point.
  • i.e., we want the genbank files. Explain the general form of a genbank file.
• what we can't get:
  • genbank sequences
  • screen grab of the process trying to get the data
• what we can get:
  • list of NCBI accession numbers
  • screen grab of the process of using the NCBI command line tool
• how we can get what we want:
  • script to download genbank files from a list of NCBI accession numbers