Extract new (alternative) transcripts from stringtie output

julia · February 11, 2020, 4:02pm

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

Alignment with HISAT2
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

Julia

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Extract new (alternative) transcripts from stringtie output

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