I know my samples are from C57BL6.
Should I use the specific for C57BL6 or just generic mus musculus 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?