Starting the pipeline with a count matrix

[lauracubitt]

Hi! I was wondering whether it's possible to start the snakemake pipeline at the point of an already processed count matrix? I have some pre-processed spatial data already, and was wondering if it were possible to start with this instead of the fastqs? Thank you!

[nukappa]

Hi @lauracubitt , it is also possible to provide a count matrix during setting up of the samples. I believe this has to be a raw count matrix and not normalized. See also here. Note that we haven't tested this feature for quite some time, so if you encounter unexpected behavior please let us know.

[lauracubitt]

Ah I hadnt spotted that option - thank you! I'll let you know if I come across any unexpected problems. Thanks for the quick reply!