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

[Carson Holt]

No it is the protein to protein blast you need (which is where cross species homology occurs). Since the proteins come from the transcripts, doing a transcript translation blast (blastx in this case) would be redundant as well as less accurate because of how artifacts of a six frame translation reduce significance of the alignment.

—Carson


> On Sep 19, 2016, at 4:46 PM, Xabier Vázquez Campos <xvazquezc at gmail.com> wrote:
> 
> 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 <mailto: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 <mailto: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 <mailto: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 <mailto: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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