Nature Scientific Reports vs. BMC Genomics
This is too long for a comment, so I post it here. And these are my personal views, someone else might handle this different. I would submit the paper to BMC Genomics for some reasons:


The editor offered to transfer the paper, so you get past the
editorial review. This is not guaranteed for Nature Scientific Report
(NSR). You still have to get through the peer review, but this is not
different between both journals.
Honestly: Forget about the difference in the Impact Factor. Both are 
medium range impact factor journals closely located together. My most
cited paper is published in such a medium impact journal, today you 
find papers by a Medline search, so this doesn't matter anymore 
(besides prestige). Additionally a lot of citations will raise the 
journals impact factor in the future. I would understand this 
argument when you would have to choose between Nature and BMC 
Genomics, there is quite a difference.
If your work fits better into BMC Genomics the chance for acceptance
is higher, so I would go there. This is of course always a point of
consideration. The same is true for your CV.


If you have the chance to do the decision for yourself without angering your supervisor too much, I would go for it. Even better would be to convince him.