De Novo Assembly - GTF/GFF File

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4.5 years ago

arussell3483 ▴ 30

Hello,

I am doing an RNA-Seq study on a non-model organism that has a published transcriptome, but no genome and no GTF file. If I were to use De Novo assembly (for example, trinity tools) is there a way to generate a GTF file? I understand that I can use tools like Bowtie, RSEM, and/or EdgeR for transcript abundance and quantification after the de novo assembly - is it possible to create a GTF file this way?

Thank you!

RNA-Seq De Novo GTF • 2.4k views

ADD COMMENT • link 4.5 years ago by arussell3483 ▴ 30

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Run TransDecoder on your de-novo transcriptome

ADD REPLY • link 4.5 years ago by Juke34 8.9k

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Thanks for the tip! If I understand correctly, it looks like TransDecoder can create a GFF file, so then I need to find a way to convert that to GTF format. Would you agree?

ADD REPLY • link 4.5 years ago by arussell3483 ▴ 30

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Lot of tools accept both GFF and GTF. If you really need a GTF pick the tool of your choice from this list.