GFF3 file -- making graphs and getting annotations
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10.2 years ago
st.ph.n ★ 2.7k

I've been recently trying to annotate a de novo assembled transcriptome from Trinity. I've been using Maker to annotate and try to 'train' the predictors. I'm also running interproscan v5, and after will update the .gff file. What I need to know is how to evaluate/analyze/parse the .gff3 file that is outputted from Maker. I know Maker suggests to use JBrowse, but I'm looking for something a little different. Is anyone aware of a tool available to get annotations and make graphs similar to how Blast2GO outputs?

gff3 annotation transcriptome genes • 4.3k views
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Try to load your gff3 in IGV. You can find your data in figures there. But, I dont think It will generate the graphs like Blast2go.

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@Prakki, I wanted to avoid GUI's if I could. Are you aware of a "parser" to pull out the annotations for each transcript ID?

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"Make graphs similar to how BLAST2GO outputs?" Could you be a little more specific? What exactly would you like to visualize?

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Maybe not even graphs, per se. I want to be able to get the annotation per transcript described in the .gff3 file. There doesn't seem to be much in ways of analyzing a .gff3 file other than Apollo or JBrowse, where one can view the annotation, given the loci, for the transcripte/genome that has been annotated.

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"Get the annotation per transcript." Again, what you need isn't particularly clear. The annotation of the gene (exon/intron) structure is provided in the GFF3 file. Are you talking about functional annotation, because that is not within Maker's scope of functionality.

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What is the best way to do functional annotation of Maker output (GFF/transcripts/proteins) ?

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