[maker-devel] Using Augustus with MAKER

[Michael Campbell]

Hi Julian,

Since you are annotating a primate I would use the pre-trained human
parameter for augustus. Here is what I would try first

 genome=data/hsap_contig.fasta    # contig file from example data
est=data/mRNAs.fa    # RNAs filtered to just mRNAs
protein=data/protein.fa
est2genome=0
protein2genome=0
augustus_species=human

You could also use one of the mammal HMMs packaged with SNAP as well, or
use the output from the above to train SNAP. There are tutorial that walk
through these steps here:

http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Main_Page

There is also a current protocols in bioinformatics article for using MAKER
can may help you get started as well.

http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0411s48/abstract

Good luck,
Mike

On Tue, May 19, 2015 at 1:51 PM, Julian Egger <julian.egger at omahazoo.com>
wrote:

>
> I am trying to use Augustus in MAKER to help with annotating as many genes
> as possible from genomic reads of a primate sample.  I am new to using gene
> prediction tools such as SNAP and Augustus, but was told Augustus would be
> better for primates.  I tried using reference mRNAs and protein sequences
> from NCBI on the sample contig file included with the MAKER software and it
> ran ok.  My question is how do I now use the output to train Augustus
> iteratively and thus create a file set of annotations from my original
> input?
>
> After creating the control files with maker -CTL, the only configurations
> I made to maker_opts.ctl were:
> genome=data/hsap_contig.fasta    # contig file from example data
> est=data/mRNAs.fa    # RNAs filtered to just mRNAs
> protein=data/protein.fa
> est2genome=1
> protein2genome=1
>
> I will eventually replace the contig file with our scaffolds file from the
> assembly.  I know the output created a gff file along with protein and mRNA
> files.  Do I then need to change the maker_opts file to account for the new
> files and if so how and what should the maker__opts file look like now?
> Was Augustus supposed to be set up on the initial maker run or do I wait
> until the second run after est2genome and protein2genome were used to
> initialize training for Augustus and how do the configurations change
> between multiple iterations because I have a solid annotation set?
>
> Sorry for all the questions, newbie here with a lot of data to work with.
>
> Thanks
>
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>


-- 
Michael Campbell MS, RD.
Doctoral Candidate
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:585-3543
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