huangyh09/brie

Brie-quant input

gabee-chan opened this issue · 2 comments

gabee-chan commented

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!

huangyh09 commented

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

huangyh09 commented

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