Question about the loom file

[yzhou666]

Hi!

I have been recently following your helpful tutorial and I have run into some problems. I am relatively new to python and would love to have some help!

First, my question would be about my loom file. I used kb to generate the loom file and ran it fine but it does not really seem correct.

In[15]: sample_1
Out[15]:
AnnData object with n_obs × n_vars = 191684 × 22582
obs: 'barcode'
var: 'gene_id', 'gene_name'
layers: 'matrix', 'spliced', 'unspliced'

Isnt usually for a loom file, it contains a lot of informations already (ex: clusters, X_pca,...)? For me, I only have these few identities inside. Did i miss some steps that let me transfer all the information about the objects from Seurat?

And after filtering the cell and concatenating my samples, I am only left with 477 cells. Is it normal to lose so many cells to filtering?

In[24]: sample_1
Out[24]:
AnnData object with n_obs × n_vars = 477 × 22582
obs: 'batch'
var: 'gene_id', 'gene_name'
obsm: 'X_umap'
layers: 'matrix', 'spliced', 'unspliced'

Thank you so much for your help!