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                                            qijt123

'WARNING: infer_data failed for target Hsf1' Retry (10/10). Failure caused by ValueError('Cleaned TF matrix is empty, skipping inference of target Hsf1.').

Hi @SeppeDeWinter Thank you for your reply! **My code:** ```python def run_scenic(adata, tf_names, DATABASES_GLOB, MOTIF_ANNOTATIONS_FNAME): exp_matrix = pd.DataFrame(adata.X.toarray(), columns=adata.var.index, index=adata.obs.index) db_fnames = glob.glob(DATABASES_GLOB) def name(fname): return os.path.splitext(os.path.basename(fname))[0] dbs = [RankingDatabase(fname=fname,...

Application of SnapATAC2 on Paired-tag data

@yoshihiko1218 Have you generated a fragment file successfully? Because I am also dealing with Paired-tag data, I have the same problem as you.

Questions about the LR-TF database

Thank you for your timely reply. I can understand your hypothesis, which is very reasonable. I have another question: Is TF's influence on TG positive? Looking forward to your reply!