how to subset cells on a pycisTopic object?

[Melody-cell]

how can I subset cells on a pycisTopic object?
Did anyone know how to do it?

[SeppeDeWinter]

Hi @Melody-cell

There is a .subset method that you can call on the object.

Best,

S

[Melody-cell]

hi, @SeppeDeWinter
but how can i run qc on a after a "sample_id_to_barcodes_passing_filters" ?

[Melody-cell]

If i run qc and filters, then i run this:

if i want to qc after filtered , should i change fragments.files?

[SeppeDeWinter]

Hi @Melody-cell

Can you please clarify your question a bit further. I'm nut sure I'm following here ...

Best,

Seppe

[Melody-cell]

Hi @SeppeDeWinter , i mean if i want to use sample_id_to_barcodes_passing_filters to run QC step again,
( this step:
!pycistopic qc
--fragments data/fragments.tsv.gz
--regions outs/consensus_peak_calling/consensus_regions.bed
--tss outs/qc/tss.bed
--output outs/qc/10x_multiome_brain )
how can i do it ?

[SeppeDeWinter]

Hi @Melody-cell

I see, so you want to run the QC on a subset of cells?
In that case you have to use a filtered fragment file indeed.

But I'm not sure why you would want to do this? You can also subset the QC stats afterwards (for instance for visualisation purposes).

Best,

S

[Melody-cell]

Hi @SeppeDeWinter ,
OK, I see. Another question is that if i want to use the upper part of the tutorial as a qc tool, can I use just fragments files to do it without cell type annotations?