[maker-devel] Using Augustus with MAKER

[Julian Egger]

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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