I am really confused about the differences between genomes released by UCSC and Ensembl. What is the difference between them?
For example, mirBase has this miRNA annotation of mice:
Chromosomal coordinates of Mus musculus microRNAs
# microRNAs: miRBase v21
# genome-build-id: GRCm38
# genome-build-accession: NCBI_Assembly:GCA_000001635.2
If I mapped my reads using UCSC mm10 genome can I do the count using this annotation? Or should I do the mapping using Ensembl GRCm38.p4 genome?