Getting unmapped reads using Hisat2
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
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Liftedkris •
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