I download 30 coding sequences genomes of different species from Ensembl or NCBI. In order to eliminate the transcripts and isoforms I used cd-hitest first and then I passed the files through TRANSDECODER.
In TRANSDECODER v.5.0.2 I did step 1 and 3, but the final file fasta.transdecoder.cds comes out with ambiguous characters like S,R,W,K,Y
I would like to know how I can solve this problem, because I have to run OMAbrowser later on.
Best regards, Daniela