[maker-devel] promiscuous mapping during annotation liftover

[Maxwell C Coyle]

Hello!

I’m using Maker to map forward annotations to a new genome assembly in a species of choanoflagellate. I followed the protocol from Campbell 2014, creating a transcript FASTA file from my old GFF3 file and using this as the only EST evidence. I set est2genome=1 and est_forward=1. The Maker ran great, except it seems that many of the old transcripts are mapping many places in the new assembly, up to 100+ times, so that my gene count has inflated from 11,624 to 25,905. Of the most highly multiply mapped genes, many but not all are rRNA genes.

I was wondering if there is a setting or tweak I can make so that each transcript maps uniquely to its best location in the new genome? Or maybe tweaking the exonerate stringency? This is not the final annotation step, as I will also be using RNA-seq evidence to improve my gene models after liftover.

Thanks for your help!

Best,
Max

Max Coyle
PhD Candidate, King Lab
Dept of Molecular and Cellular Biology, UC Berkeley



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