Hi,
I have been using HISAT2 indexer builder to build my customed reference genome, and I would like to include the gene model information (gff3). However, HISAT2 indexer only allows the outdated gtf file. I thought HISAT2 is a very updated aligning tool already.
BTW, does anyone know a convenient tool to convert gff3 to gtf? Thanks. 
Hi @YONG_JIA
Many of the underlying tools wrapped for Galaxy require GTF reference annotation format and do not support GFF3.
Converting GFF3 to GTF is very tricky to do correctly. Galaxy does not have a tool yet for this yet, although it has been discussed.
You could try the tool gffread Filters and/or converts GFF3/GTF2 records however please do note that is deprecated and may not create a GTF with all of the proper annotation tags created (will not meet the formatting requirements that tools need).
Your best way forward is to find a current source of GTF annotation that matches your genome. If your preferred source only offers GFF3, then you could write to them and ask for options. Maybe they would be willing to create/make one publically available (many data sources already have in response to requests).
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