Off topic:Getting unmapped reads using Hisat2

Question

[Liftedkris]

Hello all, i am running a dual seq analysis. I used Hisat2 to map my fastq files with the reference genome but the challenge I have now is obtaining the unmapped reads as this will be needed for mapping to the fungal reference genome that I am also required to do since it is a dual seq. Please is there any command for this?

Handle my case as a novice thanks