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

[Xabier Vázquez Campos]

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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