Velocyto .loom file creation

[AlessiaLeclercq]

Hello,
I'm trying to reproduce the .loom file for the 10X embryonic E18 Mouse Brain using velocyto CLI and compare it with the one you provide.
I run the 10X command on the folder containing the "filtered_feature_bc_matrix" and the "GEX position-sorted alignments BAM" (from cellranger arc output) using the mm10 reference .gtf file.
However, when I try to compare the resulting .loom file with yours (using scanpy) the annotated data objects have different results for the X matrix and the spliced/unspliced layers.
Did you use any expressed repeats annotation in the CLI command?

[danielee0707]

Hi, we didn't use expressed repeat masks when running Velocyto.