[maker-devel] question regarding alternate splicing annotation

[Walter Eckalbar]

Hi Maker developers,

I am trying to expand on some current annotations that are already quite
good, but only predict protein coding sequence and one isoform per gene, to
add UTRs and alternative splice forms from cufflinks data.  To do this I
put the current annotations in both the model_gff and pred_gff field, plus
the cufflinks gff3 for the ests (as I noticed was suggested in a previous
email).  I've left everything else as default, except changing
alt_splice=1. I am watching the progress of the *.gff.ann files, but I'm
not noticing alternate splicing being added, while UTRs are being picked up
(exons being added, etc.).  This is a vertebrate genome, so run times are
fairly long and I just wanted to double check if I wasn't missing
something.  Will maker go back through a second step to annotate
alternative splicing?  Or should I be trying something a little different.

Thanks,

Walter
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