File h5ad for SEVtras
Hello everyone, i'm trying to use SEVtras.ESAI_calculator to analyze my data that are the outputs of Cell Ranger. The inputs for this process are the following:
import SEVtras
SEVtras.ESAI_calculator(adata_ev_path='./tests/sEV_SEVtras.h5ad', adata_cell_path='./tests/test_cell.h5ad', out_path='./outputs', Xraw=False, OBSsample='batch', OBScelltype='celltype')
where: The first two parameters represent the path to sEV- and cell- anndata objects. sEV-anndata object comes from the output of SEVtras.sEV_recognizer. The cell-anndata object is the same as conventional single cell analysis data coming from filtered_feature_bc_matrix directory in Cell Ranger /outs.
Now, i don't understand what i have to use as input in the "adata_cell_path" field and how i can create this file starting from filtered_feature_bc_matrix directory in Cell Ranger /outs.
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yura.grabovska •
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Matteo •
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Is it not just the
filtered_feature_bc_matrix.h5inouts/? Alternatively scanpy has functionality for interacting with these objects. https://scanpy.readthedocs.io/en/stable/generated/scanpy.read_10x_h5.htmlUnfortunately it isn't. it's not similar to the file the authors loaded as a test. i don't know how to go ahead this problem, I would like to know if there is anyone who has had to do what I am doing.
Have you tried contacting the authors of the SEVtras paper?