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

bioinfo-biols / SEVtras

sEV-containing droplet identification in scRNA-seq data (SEVtras)

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Can anndata be used as the input file for part I for SEV recognition? #27

Open giuliaelgarcia opened 1 month ago

giuliaelgarcia commented 1 month ago

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 commented 1 month ago

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.