Making a "reference" proteome from RNA-seq data

Question

[davidstupski]

I'm trying to get at a list of all the amino acid sequences from RNA-seq data similar to the reference proteomes here, http://www.ebi.ac.uk/reference_proteomes, however, when I try TransDecoder, and open my long_orf.pep file most of the amino acid sequences don't begin with a methionine, has anyone else had this problem?

[Devon Ryan]

My guess is that you used the mRNA sequence rather than just the CDS.