CDS length not divisible 3

[DEYANIK]

Hello !,
I want to use TOGA for genome annotation and I downloaded the reference genome, but the problem is is that more than 50% of the CDS are not the multiples of 3.
Can you please guide me in this regard?
Thank you.
with regards,
Anik

[MichaelHiller]

Hi Anik,

you mean no divisible by 3 in the input or the query annotation?
Do you talk about exons or spliced transcripts (all coding exons combined)?