TRANSDECODER v5.0.2 - nucleotide sequences with ambiguity characters S,R,W,K, Y

Question

[dtejadamartinez]

Hello,

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.

Thanks,

Best regards, Daniela

Answer 1

[lieven.sterck]

Those UIPAC code base will probably have been their prior to the TransDecoder step as TransDecoder is not changing anything to the DNA/mRNA sequence itself. You should check that it was not cd-hitEst that introduced them or that they were even already present in the original genomic data you downloaded.

To get rid of them you can simply replace them with Ns , you're loosing information but most downstream software should be able to deal with Ns .