Drosophila transcripts from flybase different to CDS from ENSEMBL?

Question

[fcamus]

Hi there,

I have been working with the flybase drosophila transcriptome (dmel-all-transcript-r6.19.fasta) but have downloaded the ENSEMBL CDS file (which I am naively assuming that is similar to the transcriptome).

I am aligning my RNASeq reads to both files. For the flybase I get 85% of my reads mapping to the transcriptome, but only 50% of reads mapping to the ENSEMBL CDS file.

why is that?