Hi all,
I am afraid I have a silly question but I am really confused.
I am now trying to construct a de novo gene model for my species using augustus.
I ran augustus with "--genemodel=complete" option as below:
augustus --species=mySpecies --exonnames=on --codingseq=on --protein=on --extrinsicCfgFile=extrinsic.M.RM.E.W.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).
Does this kind of thing occur commonly or can it be attribute to my fault at any steps of augustus?
Best,
evolver
I am afraid I have a silly question but I am really confused.
I am now trying to construct a de novo gene model for my species using augustus.
I ran augustus with "--genemodel=complete" option as below:
augustus --species=mySpecies --exonnames=on --codingseq=on --protein=on --extrinsicCfgFile=extrinsic.M.RM.E.W.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).
Does this kind of thing occur commonly or can it be attribute to my fault at any steps of augustus?
Best,
evolver
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