Extract diversity data

General
1

Hello, I would like to have the diversity data of my analysis in excel, but within the files in the results folder I do not see any file with this information.
Is there any way to get this data?

Thanks
David

2

Hi David, can you explain what exactly you mean by diversity data? Do you mean the data as presented in the entropy panel when viewing an auspice.json like this?

Screenshot_2022-06-01-08-33-30-17_e4424258c8b8649f6e67d283a50a2cbc
Screenshot_2022-06-01-08-33-30-17_e4424258c8b8649f6e67d283a50a2cbc1080×670 89.3 KB

What workflow do you run? Your own augur pipeline or do you just view a build using auspice?

3

yes, I would like to have that data to obtain an average and obtain the places with the highest entropy, since doing this only with the view is tedious.

I use normal workflow.

4

Open your auspice.json file in auspice.us, press the d key and select Genetic diversity data.

Then you get your diversity data in TSV format.

I hope that helps!

image
image1298×522 79.6 KB

Unfortunately, I think it’s just what one sees at the moment, so if you want all 4 combinations of {AA,NT}x{entropy,events} it takes 4 downloads.