How to preprocess scATAC-seq data using pycisTopic

[wdg118]

Hi @SeppeDeWinter ,

In relation to preprocessing with pycisTopic, do we have to do all the steps in https://pycistopic.readthedocs.io/en/latest/notebooks/human_cerebellum.html# or there a particular point we stop? Do we stop after saving cisTopic object or do we continue on all the way to clustering and visualization, topic binariation and & QC, Differentially accessible regions, save region sets, gene activity, label transfer and exporting to loom?

Thanks,

wdg118

[saisomesh2594]

Any clarity on this would be great !