[maker-devel] Few alternative isoforms when alt_splice=0

[Ju Roscito]

Dear all,

I have a question about the behaviour of alt_splice option, seems there’s not much about it on the forum.

I have run a single round of MAKER (2.31.9) on a vertebrate genome, with trinity mRNA data and mapped proteins from closely-related species. I set alt_splice to 0, but still got from two to four mRNAs for ~20 out of the 19.000 predicted genes. Has someone also seen the same? Any idea why would that happen?

Thanks a lot in advance.