GENCODE reference & annotation with UCSC repeat masker

[zakieh-tayyebi]

Hi! I have used GENCODE reference sequence (GRCm38.primary_assembly) and gtf annotations (gencode.vM25.primary_assembly) to align and count my Smart-Seq2 scRNA-seq samples. I couldn't find repeat masker annotations corresponding to this assembly, so I downloaded the repeat masker tracks from UCSC (mm10_rmsk.gtf). I was wondering if it's ok, for Velocyto, to use the UCSC repeat masker alongside the GENCODE/Ensembl annotations. Thank you!