Question: De Novo Assembly - GTF/GFF File
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gravatar for arussell3483
4 months ago by
arussell348320
arussell348320 wrote:

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 gtf de novo • 233 views
ADD COMMENTlink written 4 months ago by arussell348320
1

Run TransDecoder on your de-novo transcriptome

ADD REPLYlink written 4 months ago by Juke344.8k

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 REPLYlink written 4 months ago by arussell348320
1

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

ADD REPLYlink written 4 months ago by Juke344.8k

Thank you, that's very helpful!

ADD REPLYlink written 3 months ago by arussell348320
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