Hi all,
Is there a way to download titer measurements used in the seasonal influenza build? I notice that these measurements are stored in the fauna database but I don’t know how to gain access to it. Alternatively, is there a functionality in Augur that can allow me to pass a test strain name and obtain its titer measurements against multiple sera? Any help/suggestion is greatly appreciated!
Hi @Jane, unfortunately, we can’t share the raw titer measurements publicly due to data sharing restrictions requested by the original data providers. The fauna database we use to download those measurements is our internal Nextstrain database for those data. There isn’t a standard path for publication of these data, but you can find previously published data from Bedford et al. 2014 on GitHub.
So I have csv files that were parsed from the published WIC-Crick reports. How do I put these in the format that the nextflu pipeline uses? I was able to get a rethinkdb instance working, but initializing the database is a blocker. I am not sure if the fauna repository has any scripts from creating the necessary tables in tdb with the necessary fields. Is there a basic script I can easily modify to convert the csvs into one csv file?