Generally the transcripts built from RNA-Seq data is not completed and lacks beginning or ends sometimes. It might not have the regular start codon in the transcripts. What is the best or most convenient way to identify a premature stop codon in the transcripts? Translate into protein first, pick up the longest protein sequence and identify the stop codon?
Hi Wenbin
That depends on the amount of information that you have on your organism. If you have a good quality reference gene/CDS set you can refer to the start codon of the gene model as annotated in the reference set.
If that is not the case, the main problem is that you have three possible phases for your amino acid codons. The conservative approach is to search for stop codons in any phase. Alternatively, if you know that your transcript has a well-annotated ortholog in a closely related organism, you can refer to the complete CDS of the closest organism.
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