Question: GFF3 file -- making graphs and getting annotations
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6.1 years ago by
Philadelphia, PA wrote:

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?

ADD COMMENTlink written 6.1 years ago by

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.

ADD REPLYlink written 6.1 years ago by Prakki Rama2.4k

@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?

ADD REPLYlink written 6.1 years ago by

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

ADD REPLYlink written 6.0 years ago by Daniel Standage3.9k

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.

ADD REPLYlink written 6.0 years ago by

"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.

ADD REPLYlink modified 6.0 years ago • written 6.0 years ago by Daniel Standage3.9k

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

ADD REPLYlink written 5.9 years ago by geek_y11k
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