Hello, Featurecounts expects
GTF as the input format and will fail with
Convert Formats >> gffread might be an option. The tool is deprecated at https://usegalaxy.org but still active at https://usegalaxy.eu. You’ll need to carefully inspect the output and possibly make other changes to get the data into a standardized
GTF format that meets the other criteria (many advanced options are specifying what features to count on, gene/transcript attribute content/format – and your data needs to match up).
GTF formatting and related data manipulation help:
You also might want to consider using a public Galaxy server that is domain-specific for miRNA analysis. Please see this archived Galaxy Biostars post for details and links: https://biostar.usegalaxy.org/p/28003/index.html
Contacting the MiRBase authors is also an option – they could have alternative advice for obtaining the annotation data in
GTF format. Please find the contact information at the bottom of this page: http://www.mirbase.org/ftp.shtml
All (known!) Public Galaxy servers: https://galaxyproject.org/use/
The EU team may post back with additional suggestions. Thanks!