[maker-devel] Short Introns

[UMD Bioinformatics]

Hello,

We are preparing two submission for NCBI, nightmare. However some of our MAKER gene models have short introns that are being flagged by NCBI. In one species we have >400 introns smaller then 20bp which is almost biologically impossible. I know we can set max intron length in the opts.ctl file but can we set a minimum intron length?

I saw yesterdays posts that mention this is a result of the external ab initio predictors but I didn’t see an indication as to which predictor and how to change that setting.

from yesterday:
*These are just short introns (intron size is under control of the ab initio
predictors) -->   438 ERROR:   SEQ_FEAT.ShortIntron

Cheers
Ian