Error with downstream tasks from genome = BSgenome.Mmusculus.UCSC.mm10

[alifarhat40]

Dear scMEGA team,

Thank you for this great package. I am currently going through the tutorial, and am currently facing an issue regarding the naming conventions for the mouse genome. When using ChromVAR with:

seurat_LTHSC <- AddMotifs(
  object = seurat_obj,
  genome = BSgenome.Mmusculus.UCSC.mm10,
  pfm = pfm,
    assay = "peaks"
)

I get motifs with varying capital and lower case, composite motifs, etc ..
And the gene names in my object follow the mm10 convention with capital letter first letter then small case the rest.

So when I reach functions like:

sel.tfs <- SelectTFs(object = seurat_obj,
                     tf.assay = "chromvar", 
                     rna.assay = "RNA",
                     atac.assay = "peaks",
                     return.heatmap = TRUE,
                     p.cutoff = 0.05,
                     cor.cutoff = 0.1)

It cannot connect the motifs to the gene RNA names and get almost nothing.

I end up having to do a lot of preprocessing like: break up composite motifs, remove "duplicates", convert them to title case, etc ..
This process does seem to work but I am worried I might be missing out on important functionality from scMEGA.
Have you had this issue before? Any tips or recommendations?

Thanks in advance.