About extracting CDS and PEP from GFF files obtained from TOGA

[SWei2333]

Hi Recently, I've been using annotation files for some species obtained via the TOGA method from Zoonomia. When I attempted to extract CDS and PEP from these annotation files and genomes, I found that more than half of the CDS sequences extracted using itools were not multiples of 3. Upon inspecting these sequences, I discovered that half of them had incomplete stop codons, with only one or two bases remaining. The other half ended with TGA but were still not multiples of 3. The reason for this is currently unknown.

Do you have any suggestions for this issue? Thank you very much.

Best wishes