I have got raw count of mouse RNA reads. In order to calculate the FPKM, I obtained the length of transcripts (CDS + UTR) of the genes through BioMart. And then for each gene I selected the longest one. However, later I found the alignment was mapped to an old version of genome (mm9). But the information I got from BioMart is on a new version of genome (i.e., mm10). And I found from the the web site of Biomart, I can only achieve CDS length (but not transcript length) for a old ensemble corresponding to mm9.
So I want to know
(1) is there a relatively easy way to get the length of transcripts for mm9, given the gene ensemble ID?
(2) If there is no easy ways, is it good enough to use the transcript length from mm10 to calculated the FPKM? I think the gene length from different version of genome should be the same or quite similar, right?