spacexr icon indicating copy to clipboard operation
spacexr copied to clipboard
verified publisher icon dmcable

Question about spot filtering in create.RCTD step

Open Yijia-Jiang opened this issue 1 year ago • 1 comments

In create.RCTD step, we can set the threshold for counts_MIN and UMI_min, what is the difference between counts and UMI here? It seems in the restrict_counts function, both refer to the column sum, which is sum of counts for each spot. Then why are we having two different thresholds here?

Yijia-Jiang avatar Nov 26 '24 17:11 Yijia-Jiang

UMI_min filters cells. counts_MIN filters genes.

dmcable avatar Jul 19 '25 00:07 dmcable