[maker-devel] Maker consensus
Diana LeDuc
diana_leduc at eva.mpg.de
Fri May 10 12:16:34 MDT 2013
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
> <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/zff2augustus_gbk.pl
> <https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl>
>
> Thanks,
> Carson
>
>
>
> From: Diana LeDuc < diana_leduc at eva.mpg.de <mailto:diana_leduc at eva.mpg.de> >
> Reply-To: Diana LeDuc < diana_leduc at eva.mpg.de
> <mailto:diana_leduc at eva.mpg.de> >
> Date: Friday, 10 May, 2013 1:41 PM
> To: < maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org> >,
> Carson Holt < carsonhh at gmail.com <mailto:carsonhh at gmail.com> >
> Cc: Torsten Schoeneberg < torsten.schoeneberg at medizin.uni-leipzig.de
> <mailto:torsten.schoeneberg at medizin.uni-leipzig.de> >, Gabriel Renaud <
> gabriel_renaud at eva.mpg.de <mailto:gabriel_renaud at eva.mpg.de> >, Janet Kelso <
> kelso at eva.mpg.de <mailto: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=ENSTGUG00000000198|ENSTGUT00000000219|DSCAML1-2039;Target=ENSTGUG00000000198|ENSTGUT00000000219|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
> <mailto:carsonhh at gmail.com> > wrote:
>
> > > I'm sorry I don’t' 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 <mailto:diana_leduc at eva.mpg.de>
> > >
> > Reply-To: Diana LeDuc < diana_leduc at eva.mpg.de
> > <mailto:diana_leduc at eva.mpg.de> >
> > Date: Friday, 10 May, 2013 10:44 AM
> > To: < maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org> >
> > Cc: Gabriel Renaud < gabriel_renaud at eva.mpg.de
> > <mailto:gabriel_renaud at eva.mpg.de> >, Janet Kelso < kelso at eva.mpg.de
> > <mailto:kelso at eva.mpg.de> >, Torsten Schoeneberg <
> > torsten.schoeneberg at medizin.uni-leipzig.de
> > <mailto: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 <mailto:maker-devel at box290.bluehost.com>
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> > <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> >
> > >
>
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