[maker-devel] questions about post-processing of annotations

[Carson Holt]

maker_functional_fasta reads the results of a blast report. It must be a tab delimted blast report (-outfmt 6 under BLAST+) with unpirot as the database and the maker fasta file as the query. If you renamed the transcripts in the fasta before running maker_functional_fasta, the results in the blast report will no longer match (because they have new names). Use the map_data_ids script to fix names in the blast report if you did that.

Thanks,
Carson

> On Sep 19, 2016, at 2:30 AM, Xabier Vázquez Campos <xvazquezc at gmail.com> wrote:
> 
> Hi Carson,
> 
> I'm trying to go through the post processing step in the tutorial (GMOD2014) but I think something is not right with the functional annotation as no new information is added to the *.putative_function.* files when I run the maker_functional_gff or the maker_functional_fasta. All the fasta headings remain unchanged and the gff files don't show any change. I'm using Maker 2.31.6 by the way.
> 
> Because there are no examples showing what I should expect I'm a bit lost.
> 
> These are my files prior to the functional annotation.
> 
> FRL.all.iprscan.renamed.tsv
> FRL.all.maker.proteins.blastout.sprot.renamed.tsv
> FRL.all.maker.proteins.renamed.fasta
> FRL.all.maker.transcripts.renamed.fasta
> FRL.all.maker.trnascan.transcripts.renamed.fasta
> FRL.all.renamed.gff
> FRL.map
> 
> And this, an example of the command I'm using
> 
> maker_functional_fasta uniprot_sprot.fasta FRL.all.maker.proteins.blastout.sprot.renamed.tsv FRL.all.maker.proteins.renamed.fasta > FRL.all.maker.proteins.renamed.putative_function.fasta
> 
> Thank you in advance.
> 
> Xabi
> 
> 
> PS: the tutorial mentions to use the "standard" IPRS output but by default it gives xml, gff3 and tsv files. Which one should I use?
> 
> -- 
> Xabier Vázquez-Campos, PhD
> Research Associate
> Water Research Centre
> School of Civil and Environmental Engineering
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA

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