Hello all,
 I am working goat genome sample, completed the assembly and masking of genome. Can anyone suggest how to go do gene prediction since augustus doesnt have any ref goat for gene prediction.


Hi,
1. easy way- use on line training here "http://bioinf.uni-greifswald.de/webaugustus/training/create" and use the paramaeter for you species.

you can prepare training data set from the goat refseq files from NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Capra_hircus/latest_assembly_versions/GCF_001704415.1_ARS1/).


2. You can follow the instructions given in the following links for making custom files and training AUGUSTUS.
 "https://vcru.wisc.edu/simonlab/bioinformatics/programs/augustus/docs/tutorial2015/training.html"
 "http://avrilomics.blogspot.in/2013/04/training-augustus-gene-finding-software.html"
you can use refseq RNA and protein files from the NCBI link for getting RNA and PROTEIN files.

Notes:
I used MAKER to annotate genome initially using RNA and Protein sequences from the closest species and the GFF output from this was used to get 1) multi-exonic  2) non-overlaping 3) relatively non-close sequences (<70% identity) transcripts.
I have converted this GFF file (after filtration) to gb file format using "./scripts/gff2gbSmallDNA.pl" available in AUGUSTUS and used further according to the instructions given in above mentioned links (to be specific first link). 





