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rajewsky-lab / novosparc

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geometry.txt #19

Closed grst closed 4 years ago

grst commented 4 years ago

Hi @nukappa,

I am a bit confused with the geometry file.

I could only find this one: https://github.com/rajewsky-lab/novosparc/blob/master/novosparc/datasets/bdtnp/geometry.txt

It has 6079 lines and fails with the in-situ data. The one you have in the tutorial notebook looks a bit different, and, I assume, has 3039 lines.

geometry.txt from repo: image

geometry in the tutorial notebook: image

Could you please provide the right one? Or am I overlooking sth?

Cheers, Gregor

nukappa commented 4 years ago

Hi @grst that's the correct file, containing 3039*2 locations in (x, y, z). For the tutorial (and also the figures in the paper) truncate it to the first 3039 locations in (x, z). The embryo has a bilateral symmetry at this stage, so only half of locations have unique transcriptomes.

grst commented 4 years ago

That has worked, thanks! I can now reproduce all the figures.