[maker-devel] Maker consensus
Carson Holt
carsonhh at gmail.com
Fri May 10 12:29:32 MDT 2013
You can use any species augustus already has. If it doesn't then you train
it yourself. The species folder is pointed to by the AUGUSTUS_CONFIG_PATH
environmental variable, and is usually Š/augusts/config/species
Thanks,
Carson
From: Diana LeDuc <diana_leduc at eva.mpg.de>
Reply-To: Diana LeDuc <diana_leduc at eva.mpg.de>
Date: Friday, 10 May, 2013 2:16 PM
To: <maker-devel at yandell-lab.org>, Carson Holt <carsonhh at gmail.com>
Cc: Torsten Schoeneberg <torsten.schoeneberg at medizin.uni-leipzig.de>,
Gabriel Renaud <gabriel_renaud at eva.mpg.de>, Janet Kelso <kelso at eva.mpg.de>
Subject: Re: [maker-devel] Maker consensus
Hi Carson,
In maker_exe.ctl I would have to provide the path to augustus. Augustus has
a training set for chicken that I would use. Is it possible to specify the
species i want to use, or the only way is training Augustus myself?
Thank you!
Best,
Diana
On May 10, 2013 at 7:51 PM Carson Holt <carsonhh at gmail.com> wrote:
>
> Ok. You just ran the evidence and didn't give a gene predictor. You need to
> provide an HMM file for SNAP a species for augustus, or for rough annotations
> you can set protein3genome=1 and est2genome=1. This will try and generate
> models direct from the alignments.
>
>
>
> If you provide a gene predictor, then MAKER can talk to it about the evidence
> alignments so it can make a best gene call for the region. Then there will be
> gene/mRNA/exon model in the GFF3 file and entires in the proteins.fasta and
> transcripts.fasta. If you need to train a predictor, you can train SNAP using
> the maker2zff script and the SNAP documentation or maker GMOD tutorial. If
> you want to train augustus Jason Stajich wrote an excellent explanation as
> well as tools in a previous list message.
>
>
>
>
> list msg - http://brie4.cshl.edu/pipermail/gmod-help/2012-June/001724.html
>
> Script is in this github repo -
>
> https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2au
> gustus_gbk.pl
>
>
>
> Thanks,
>
> Carson
>
>
>
>
>
>
>
> From: Diana LeDuc < diana_leduc at eva.mpg.de>
> Reply-To: Diana LeDuc < diana_leduc at eva.mpg.de>
> Date: Friday, 10 May, 2013 1:41 PM
> To: < maker-devel at yandell-lab.org>, Carson Holt < carsonhh at gmail.com>
> Cc: Torsten Schoeneberg < torsten.schoeneberg at medizin.uni-leipzig.de>,
> Gabriel Renaud < gabriel_renaud at eva.mpg.de>, Janet Kelso < kelso at eva.mpg.de>
> Subject: Re: [maker-devel] Maker consensus
>
>
>
>
>
> Hi Carson,
>
>
>
> Thank you for the quick answer.
>
> I ran gff3_merge to merge all the gff files and this resulted in a gff file,
> which has these type of fields:
>
> scaffold32239 blastx protein_match 22905 34500 174 + .
> ID=scaffold32239:hit:976144;Name=ENSTGUG00000000198|ENSTGUT00000000219|DSCAML1
> -2039;
> scaffold32239 blastx match_part 22905 23045 174 + .
> ID=scaffold32239:hsp:2806529;Parent=scaffold32239:hit:976144;Name=ENSTGUG00000
> 000198|ENSTGUT00000000219|DSCAML1-2039;Target=ENSTGUG00000000198|ENSTGUT000000
> 00219|DSCAML1-2039 172 218;Gap=M47;
>
> In comparison to the dpp_contig test file, I am missing est2genome evidence,
> most probably because my est data set is pretty poor. I have blastx and
> protein2genome evidence though.
>
>
>
> My goal is to extract the genes that could be annotated on the scaffolds. In
> the gff files the hits overlap most of the times, I can visualize this
> properly in apollo: for example one scaffold hits DSCAML gene in both
> zebrafinch and chicken, but extracting the coordinates between which this
> scaffold fits this annotated gene is difficult from the gff. Manually curating
> the genes is also not an option, since I am trying to do this for a 1.7Gb
> genome.
>
>
>
> I hope this explains better what we are after.
>
>
>
> Thank you once again.
>
>
>
> Best regards,
>
>
>
> Diana
> On May 10, 2013 at 6:13 PM Carson Holt < carsonhh at gmail.com> wrote:
>
>
>>
>> I'm sorry I don¹t' understand question 1. You are you missing resulting
>> fasta files, correct? Did your resulting GFF3 file have any features of type
>> "gene"? Did you run fasta_merge after running gff3_merge?
>>
>>
>>
>> Could you give me more details on what you are trying to do, so I can take a
>> stab at question 2 as well.
>>
>>
>>
>> Thanks,
>>
>> Carson
>>
>>
>>
>>
>>
>>
>>
>> From: Diana LeDuc < diana_leduc at eva.mpg.de>
>> Reply-To: Diana LeDuc < diana_leduc at eva.mpg.de>
>> Date: Friday, 10 May, 2013 10:44 AM
>> To: < maker-devel at yandell-lab.org>
>> Cc: Gabriel Renaud < gabriel_renaud at eva.mpg.de>, Janet Kelso <
>> kelso at eva.mpg.de>, Torsten Schoeneberg <
>> torsten.schoeneberg at medizin.uni-leipzig.de>
>> Subject: [maker-devel] Maker consensus
>>
>>
>>
>>
>>
>>
>>
>> Dear maker developers,
>>
>>
>> I am a phD student working on de novo assembly and annotation of a bird
>> genome. I used Maker as annotation pipeline, which ran very well, and I
>> obtained different annotations with evidence from Augustus gene predictor,
>> small EST dataset from my organism and protein sequences from chicken, turkey
>> and zebrafinch. I could combine the different gff files from different
>> scaffolds into one gff file with annotations for the entire genome.
>>
>>
>> I now have two questions:
>>
>>
>> 1. What could be the reason that I haven't gotten the protein.fasta and
>> trancript.fasta files
>>
>>
>> 2. How can I obtain a consensus gene list of different evidences from maker?
>> What I would actually need is the scaffold, coordinates and annotation (gene
>> name) according to the 3 other bird species.
>> Thank you in advance.
>>
>>
>>
>> Best regards,
>>
>>
>>
>> Diana Le Duc
>>
>>
>>
>> --
>>
>> Max Planck Institute for Evolutionary Anthropology
>> Department of Evolutionary Genetics
>> Deutscher Platz 6
>> D-04103 Leipzig
>>
>> Phone +49 (0)341-3550-554
>> www.eva.mpg.de <http://www.eva.mpg.de>
>>
>>
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
>
>
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