Can anndata be used as the input file for part I for SEV recognition?

[giuliaelgarcia]

Hi, is it possible to run SEVtras part I with all the raw cellranger outputs for multiple samples already in an anndata or does it need to be run by providing the raw cellranger outputs separately?

[RuiqiaoHe]

SEVtras supports anndata formatted as h5ad files. You can specify the sample_file as the following format:

test1.h5ad
test2.h5ad
...
testN.h5ad

By the way, the input droplet-gene matrix for SEVtras should be the raw data; herein, the matrix should come from the raw_feature_bc_matrix directory in Cell Ranger outs.