Extract new (alternative) transcripts from stringtie output

Hi everyone,

I’m looking for a workflow to identify and extract new transcrits from RNASeq data in Galaxy.
What I did up to now was a genome guided transcriptome assembly

  1. Alignment with HISAT2
  2. StringTie with a Reference Annotation (-G option) with an anotation made by AUGUSTUS tool as Reference Annotation
    nowI have a .GTF file but I want to extract fasta sequence to obtain a MultiFASTA file containing protein sequences of ma transcriptom containing all the alternative transcripts.
    It would be great If someone knew how to proceed to get this fasta file!
    Have a nice day,
    Best regard