I am doing transcriptome analysis of wheat translocation lines, means they have a "big chunk of DNA" inserted into their chromosomes. The plant from where this big chunk came is a wild plant with zero genome information available about it. This wild plant is actually a relative of wheat. I want suggestion about how do I know about the foreign "dna chunk" expression in my wheat translocation lines.. I think I should look into the unmapped reads file, assemble them and then use them as potential foreign transcripts. Please suggest me something better.
If you have no genomic information, I think it might be hard to find the full piece of the added DNA. You can try to assemble the transcriptome denovo and map to the genome, in-order to check where you have inserts. But the problem here would be that its hard to be precise without long-read information, due to chimeric transcripts. Then map the unmapped reads to the transcripts in insert positions as a sanity check, and check for expression with a transcript-based approach.