I have a question regarding the denovo assembly and transcripts that were obtained from the assembly.
After denovo assembly i tried to blast the transcripts to the reference transcriptome (from a different sub species) to see if i could find any novel transcripts. After that i filtering out the novel transcripts and i blasted them to reference genome (again from a different sub species) to make sure they are there in the genome. Surprisingly only 77% of those novel transcripts found hit on the genome. I have later blasted the non genome hit transcripts to related organism and all expect few have a hit there (The non hit ones are from human contamination).
My question now is what are these transcripts that doesn't have any hit either at transcriptome level or genome level but have hit to a related organism.