genemodel=complete option
Posted: Thu Nov 19, 2015 3:22 pm
Originally posted in the old forum by Sung on 30.09.2015 - 18:28
Hi,
I ran augustus with "--genemodel=complete" option as below:
augustus --species=mySpecies --exonnames=on --codingseq=on --protein=on --extrinsicCfgFile=extrinsic.M.RM.E.W_edited.cfg --alternatives-from-evidence=true --hintsfile=hint.gff --allow_hinted_splicesites=atac --genemodel=complete genome.fa > aug.out
ant then, used getAnnoFasta.pl to extract amino acid sequences in fasta format.
However, I found in aug.out.aa file that some predicted proteins do not start with methionine(Met).
How to fix this situation?
Hi,
I ran augustus with "--genemodel=complete" option as below:
augustus --species=mySpecies --exonnames=on --codingseq=on --protein=on --extrinsicCfgFile=extrinsic.M.RM.E.W_edited.cfg --alternatives-from-evidence=true --hintsfile=hint.gff --allow_hinted_splicesites=atac --genemodel=complete genome.fa > aug.out
ant then, used getAnnoFasta.pl to extract amino acid sequences in fasta format.
However, I found in aug.out.aa file that some predicted proteins do not start with methionine(Met).
How to fix this situation?