I have RNA-seq data of a wheat translocation line which has its chromosome short arm replaced by another wild variety chromosome short arm. There is no genomic or transcriptomic information available for that wild variety. I want to see what kind of genes are expressing from the new short arm. For this I was thinking if I can do denovo assembly of the unmapped reads and then blast the assembled transcripts with nr database. I want to know if this strategy is correct or not or if there is a better way to do it.
update: number of unmapped read pairs is around 8 million, total reads were around 33 million and I used the following parameters in hisat2
hisat2 -x wheat_hisat_index -1 13R_R1.fastq -2 13R_R2.fastq -S 13.sam -p 12 --mp 8,4 --rdg 7,5 --rfg 7,5 --un-conc 13_unmapped_pairs