Brie-quant input
gabee-chan opened this issue · 2 comments
Hi!
Hope you can help me.
In your documentation (https://brie.readthedocs.io/en/latest/brie_count.html) you mention that "brie-quant is more generic and can be applied if the counting has been done, either by brie-count or other tools." I was wondering how can I format the h5ad output from a different tool to be able to use brie-quant.
The reason to use a different tool than brie-count is that I want to use 10x data.
Cheers!
Thanks for the good question!
To make a customised h5ad, you only need two layers in anndata. You could use any name as long as it is the same as your argument in --layers=LAYERS
in brie-quant. But make sure that these two layers are raw counts without any normalisation.
We are still developing a new version to support 10x data soon (brie-countX
). Will mention it here when it's officially released.
https://github.com/huangyh09/brie/tree/2.x.x
Yuanhua
Hi, just to let you know that we have released v2.2.0 supporting counting on droplet-based platforms.
See the notes in brie-count manual. Feedbacks are welcome.
Yuanhua