Constrain the outgoing reference bases alphabet to ACTGN

A repository may be lenient in the data they accept at import-time, but should be strict in what they emit at serving-time.
@fnothaft is right in that sometimes aligning to a transcriptome can be helpful for RNA-seq data, depending on the splice events that took place and what coding regions were kept.  Your reads would contain more the "exons" - depending on the splice events that took place - and thus should match closer to your transcriptome than your genome - which undoubtedly would contain more.