Dears,

I want to know whether there is difference between different genome fasta files like `Mus_musculus.GRCm38.dna.toplevel.fa` file downloaded from ENSEMBL and `chrom_mm10.fa` file downloaded UCSC. Whether we can annotate the alignment bam files (using UCSC genome as reference) with ENSEML annotations. 

Any comments and explanations are appreciated.

I would suggest reading the README file for the data. [Here is the Ensembl one.](ftp://ftp.ensembl.org/pub/current_fasta/mus_musculus/dna/README)

Generally, it is recommended that you use reference annotation and genome files from the same source.