Raw and filtered count data similar to cell ranger output.

[bk11-lab]

Hi, Thank you for the nice software. I have been trying your tool to our small nuclear RNAseq data. The first impression from running data using alevin-fry is very good because I m getting much more number of nuclei compared to result from cell ranger. However, after piping the data through Seurat, I am seeing some ambient RNA contaminations. I m wondering if alevin-fry outputs data as Raw Count Matrix and Filtered Count Matrix similar to Cell Ranger output? My idea is to run ambient RNA correction in these data using tools such as SoupX or DecontX. I appreciate your help.

BK