questions about reading data

[ikun-jinitaimei]

...: data_dir = '/work/sjp/data/'

In [23]: scalesc = ssc.ScaleSC(data_dir=data_dir,
...: max_cell_batch=1e5, # no more than 1e5 is suggested
...: preload_on_cpu=True,
...: preload_on_gpu=True,
...: save_raw_counts=False,
...: save_norm_counts=False,
...: output_dir='test_scalesc_2.9M_results')
In [24]:
In [24]: print(scalesc.adata.shape)
(2915977, 5001)
In [25]: print(scalesc.reader.shape)
(-1, -1)

scalesc.reader.shape displays (-1, -1), which is very strange, causing problems in subsequent data processing. I implore you to help. Thank you!

[haotianzh]

Hi kunkun, have you setup any cell or gene filters? I would recommend to set filters to both cell and gene as described in tutorial and try it again. You can set min_count=0 If you don't really need it.
Just let me know if it doesn't work.