To convert String tie GTF file to FASTA file

I have used tool String tie to prepare reference assembly and got output data as GTF file. For structural and functional annotation I need to convert it to FASTA format. suggest me with a tool which can be used to convert GTF to FASTA.

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Hi @Vikas_Sharma

The transcript assembly that Stringtie generates is not a full assembly that leads to a fasta output.

For a fasta output, you’ll need to assemble the reads with a tool like Trinity.

The GTN Tutorials cover the how-to. Examples below. The last one is a work-in-progress but should be useful even in the current state.


More help for Trinity is available from the tool authors. The methods are described for the command-line version of the tool but the overall protocol is the same as when running the wrapped tools in Galaxy.

Thanks!