HISAT2 human index and GTF file version incompatibility

Question

[Rituriya]

Hi All,

I have asked this 6 years ago in the same forum and no one has replied yet! So I thought of posting again with the hope of an answer -

I am surprised as to how come no one else is reporting this incompatibility - I am using HISAT2 GrCh38 release 84 version for the genome as provided by the developers and using Ensembl GTF version 113 (latest in 2024) for annotating the genes. The index was built using Ensembl v84, which is so outdated. Is it okay to proceed like this?

Thank you!

[pinheirofabiano]

you should try a response in the HISAT2 GitHub page.. it's an important question..