I did mapping of illumina raw reads to CDS transcripts and I extracted unmapped raw reads.
after that I did assembly of these unmapped raw reads. Now I want to map these assembled transcript to genome scaffold to find how many of them are able to map to genome and whether they map to different position to each others.
FINALLY will extract only those DE NOVO ASSEMBLED TRANSCRIPT which are able to map to genome but not annotated as CDS.
So my finally reference for differential gene expression will be CDS plus de novo assembled transcripts.