To set up a pipeline for processing RNA-Seq FASTQ files, you need to obtain an appropriate HISAT2 index and GTF file. Even if files from different species are used, or the genome versions of the HISAT2 index and GTF do not match, the pipeline may still complete successfully without producing an obvious error. Therefore, before running the pipeline, make sure that the correct files have been selected.
The genome version of the HISAT2 index you want to use may not match the genome assembly used by the latest Ensembl GTF. In such cases, you need to find a GTF file for the appropriate genome version in an older Ensembl release.
Finding a GTF File in an Earlier Release
Open the latest release folder and find the GTF directory for the species of interest.
For example, if the GTF directory is
https://ftp.ensembl.org/pub/release-116/gtf/
and you open the Homo sapiens directory, the URL will be
https://ftp.ensembl.org/pub/release-116/gtf/homo_sapiens/
You can then change the release number in the URL and check earlier releases, for example:
https://ftp.ensembl.org/pub/release-76/gtf/homo_sapiens/
https://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/
By going back through the release numbers in this way, you can see that the genome assembly changes to GRCh37 in release 75.