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

[Xabier Vázquez Campos]

I see. I ran blastp before starting the "post-processing of annotations"
step. I guess I should do the same with IPRS.

By the way, can you confirm If I need to blast the maker.transcripts.fasta?

Thanks a lot

On 20 September 2016 at 08:43, Carson Holt <carsonhh at gmail.com> wrote:

> You just have to make sure you ran the blast job report after renaming. If
> you ran it before then the names in the report will not match the renamed
> fasta. The blast job should be blastp (protein to protein). You can check
> by just looking at the report.
>
> —Carson
>
>
> On Sep 19, 2016, at 4:27 PM, Xabier Vázquez Campos <xvazquezc at gmail.com>
> wrote:
>
> 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
>
>
>


-- 
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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