# Extract new (alternative) transcripts from stringtie output

**URL:** <https://help.galaxyproject.org/t/extract-new-alternative-transcripts-from-stringtie-output/2964>\
**Category:** Uncategorized\
**Created:** [February 11, 2020, 4:02pm UTC](https://help.galaxyproject.org/t/extract-new-alternative-transcripts-from-stringtie-output/2964 "2020-02-11T16:02:36Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![julia](https://avatars.discourse-cdn.com/v4/letter/j/2bfe46/32.png) [@julia](https://help.galaxyproject.org/u/julia)\
**Post date:** [February 11, 2020, 4:02pm UTC](https://help.galaxyproject.org/t/extract-new-alternative-transcripts-from-stringtie-output/2964/1 "2020-02-11T16:02:37Z")

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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

Julia