I'm new to bioinformatics and having problems with RNAseq analysis.
I'm trying to use HISAT2 to align RNAseq reads to wheat genome.
Since wheat reference genome was released in Jan., I could align my sequences to the genome.
However, GFF file for this reference is not yet built, so I can't quantify transcripts.
Are there any ways to build GFF file in this situation?
Or, do I have to perform de novo assembly?