Question about "uncommon" genomes

[amitjavilaventura]

Hello!

I am working with small RNA seq data from testis in three different Mus species. Two of them have very recent genome assemblies and are not in the genomes provided by iGenomes, nor in the piSet supported genomes. Moreover, the repeatMasker website does not have them.

I was wondering whether I can install a genome by using the FASTA file with the genome assembly, the repeats (either repeatMasker annotation/sequence downloaded from UCSC or small RNA-seq FASTQs) and the gene annotation (GTF)?

Thank you very much.

Adrià.