I know my samples are from C57BL6. 

Should I use the [specific for C57BL6][1] or just [generic mus musculus][2] reference transcriptomes/genomes for alignments? 

I am worried that the file size for the reference transcriptome for C57BL6 (`Mus_musculus_c57bl6nj.C57BL_6NJ_v1.cdna.all.fa.gz`, 39.7 MB) is 22% smaller than its generic counterpart (`Mus_musculus.GRCm39.cdna.all.fa.gz`, 51.2 MB). Clearly, biologically the C57BL6 transcriptome cannot be 22% smaller than the transcriptome of some other strain, so there is something going on with the lower detalization for C57BL6??

What do I gain, what do I lose if I opt for C57BL6-specific transcriptome/genome?

  [1]: https://ftp.ensembl.org/pub/release-109/fasta/mus_musculus_c57bl6nj/
  [2]: https://ftp.ensembl.org/pub/release-109/fasta/mus_musculus/
There's some basic literature on the topic here: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010552 . Slightly improved uniquely mapped reads; though mapping parameters appear to have a stronger impact than choice of reference.

However, for *differential* expression (BL6/J untreaded vs BL6/J treated) the question isn't so much "how do the quantifications change" but "how do the logFCs change" -- and I don't see published results on this. I should imagine that, by aligning to the strain transcription, some genes might get slightly higher coverage to bump them over the soft-filtering threshold; but few (if any) logFC values should alter based on the reference.

It's probably worth doing twice just to put your mind at ease.