Almost all spaln mRNA without the final stop codon

[xiekunwhy]

Hi,

I found that almost all spaln mRNA without the final stop codon, is there a way to include the final stop codon?

here are my command lines:

makeidx.pl -inp Op-f.gf spaln -t20 -M4 -Q7 -O0 -LS -ya012 -o all_aa.gff3 -d Op-f all.aa

when I use gffread to extract cds sequence from all_aa.gff3, I found that only a few cds sequence with stop codon, only 10/50000.

Best, Kun