Which .fa files should I include when creating a ref. genome of a non-human species?

[Stina]

I intend to analyse HTS resequencing data from a capture experiment in dogs and I am trying to create a reference genome to use for the analysis. I want to use the FASTA files at ensemble. The FASTA files available here are from: chr 1-38, MT, X and nonchromosomal, but none for the Y chromosome... Should I include the MT and nonchromosomal data when creating a reference genome file? And if so, where should I place them (in what order)?

Many thanks in advance!

[mbblack]

When mapping my RNA-seq data, I make two files. One is the reference genome I am mapping to, the other is a filter reference file for reads to be excluded from mapping (mtDNA, rRNA and all non-coding sequences). Most mapping tools will let you use such a filter reference to exclude reads and thus not waste time and compute resources mapping them to the full reference genome.

[westerman]

mbblack has a good suggestion. As to your exact question of "...where should I place them..." it matters not. I suspect that most people put them after the numbered chromosomes.

[Stina]

Thanks for the advice!