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

[Xabier Vázquez Campos]

Yes, my blast output is -outfmt 6 using the Uniprot/Swissprot as database.
I used the maker protein fasta file as query (should I do the same with the
transcripts?).
According to the tutorial the steps are:

maker_map_ids
map_gff_ids
map_fasta_ids (for maker protein and transcripts)
map_data_ids (for blast and iprs output)

and then the maker_functional_* steps.

So, the rename steps are before the maker_functional. Are you saying
it should be the other way around?





On 20 September 2016 at 08:07, Carson Holt <carsonhh at gmail.com> wrote:

> 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
>
>
>


-- 
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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