[Cg-pipeline-users] prediction question

[kokwei <kok...@gm...>]

Hello,

I notice that for cg pipeline, assembly linker used for joining the 
contigs/scaffolds during prediction is included in the gene model 
instead of just forming as a linker (I found VXX as 5' and XXHT as 3' of 
some gene models). All the coordinates of gene models also have an 
offset of 36 bp due to the inclusion of the linker at the 5' end of the 
assembly sequence.
Is it possible to remove those linker from the gene model during 
pipeline execution and output correct location? Thanks.