Finding X scaffolds in a genome assembly

[desmodus1984]

Hi,
I would appreciate if you can help me. I am interested in demographic inference of bats. I assembled a reference genome, and I have downloaded mouse and human X and Y sequences; the human X chromosome is by far larger than any of my scaffolds because I used a reference that lacks centromeres and telomeres. The mus X and Y are not complete, just the X is as large as my largest scaffold. I am a beginner and I would like to know what should I map with meryl and what should be my query.
How should I retrieve the mapped reads - with samtools?

Thank you very much;