Question: (Closed) Getting unmapped reads using Hisat2
gravatar for Liftedkris
17 months ago by
Liftedkris20 wrote:

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

rna-seq tool • 1.2k views
ADD COMMENTlink modified 17 months ago by ATpoint36k • written 17 months ago by Liftedkris20

Hello citynsukka!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.


PS: See the linked thread for extracting reads that are mapped/unmapped from a SAM/BAM file.
ADD REPLYlink written 17 months ago by ATpoint36k
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