I mapped de novo assembled transcript to genome using GMAP but still large no. of transcripts showing similarity with draft genome sequences. My aim is it extract unique sequence which do not mapping to draft genome?
I have 32 paired end RNA seq libraries. Can I take all raw reads R1 and R2 reads in two separated files and is it possible to map those raw reads to Draft genome and to extract unmapped R1 and R2 reads in two separete files and followed by de novo assembly?
Please suggest which software should I use to complete this analysis?