I always can not choose from the build-in reference genomes.

Anyone has the same problem here? or knows the solution?

Any suggestions are appreciated.

Thanks.
 

Hey cooleel,

Short answer to your title: Yes, HISAT2 is working!

Good news, the question you asked has been before and Jen has given a detailed answer:

HISAT2 - no reference genome available

As she says, you can still use a custom reference genome by selecting "Use a genome from history" and uploading the corresponding fasta file.

Thanks for the answer！