I have a bit of a predicament. I'm a student currently analyzing RNAseq data. I usually go for de novo assembly;however, recently a reference genome has come available for our organism. The problem is, the genome is incomplete, it's a draft and about a third to a quarter of it is estimated to be missing. I am obtaining about 10,000 extra genes when using de novo transcriptome assembly, and as such this number of unigenes comes closer to the 100% estimated amount of genes.
Do I go with de novo assembly using trinity based on my deep sequenced RNA-seq reads OR do I map to the genome even though it's a draft which is quite incomplete.
Please let me know what would be best.