Cannot find correspondence of the input data

[cindyway]

Hi, Thank you for providing the detailed code for use.

I have noticed a discrepancy between the number of spots mentioned in the MERFISH tutorial and the paper. I assume these might be different datasets. However, when I checked the provided data link, I couldn't find the 58,022 snRNA cells and 4,951 spots mentioned. Furthermore, in GSE115746, there are approximately 15,000 cells in VIPs but the paper said 11,759 single cells need to be mapped. The 1,550 cell barcode count was provided in STARMap, but only 1,207 positions were given. Could you please explain how to filter for consistent cells and provide more detailed clarification on the handling of cell selection?

[gaddamshreya1]

Hi @cindyway, I'm working on finding the exact filters that were used for these datasets!

• Meanwhile, a more general method for filtering cells is described in this tutorial for single cell RNA sequencing data.
• For spatial datasets, to filter spots that are away from tissue sections we use this density based clustering package.