[maker-devel] Alternative splicing in MAKER

[Lior Glick]

Hello,

I am working on a computational pipeline which involves genome annotation.
Based on helpful advice I got in this mailing list before, I make two
consecutive runs: the first is a liftover run with est2genome=1 and no
ab-initio prediction, while the second run takes liftover results and adds
ab-initio predictions, supported by protein and transcript evidence.
In both runs, I get results which I find confusing regarding alternative
splice variants prediction, but the behavior is different in each run.

In the liftover run, I use est2genome=1, alt_splice=1 and no ab-initio
preduction.
The resulting gff indicates many overlapping genes, coming from ESTs
(transcripts actually) of different splice products of the same gene. Of
course MAKER has no way to know that, but I was expecting that since the
genes are highly overlapping, they will be grouped together as different
mRNA features under the same gene.
In the second run, I use est2genome=0,  alt_splice=1 and Augustus for gene
prediction. Results of the liftover run are provided to the pred_gff
parameter. In this case, it seems that overlapping genes are squished
together, so I only get one gene with one mRNA.
Please find attached maker_opts.ctl files for both runs, and GFF files
demonstrating the issue (one gene example).

Could anyone please explain how this works? Why is the behavior different
between the runs? Any way to get MAKER to behave the way I expected?

Thanks a lot!
Lior
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