[maker-devel] Intron lengths below minimum cutoff

[Carson Holt]

Looking through old messages, it looks like this one fell through the cracks. The min_intron parameter is for exonerate alignments (gets past directly to the algorithm). However gene predictors like SNAP and Augustus can still call introns of any length they wish (doesn’t affect them). So you can still get shorter introns in the model, you just won’t get short introns from exonerate or in the evidence hints passed to SNAP and Augustus.

—Carson


> On May 29, 2020, at 3:49 PM, Trojahn, Shawn Michael <shawn.trojahn at wsu.edu> wrote:
> 
> Hello,
>  
> I have been having a problem with the final annotation coming from Maker2 where I have a few thousand introns that are below the minimum intron value I have set. Most of the exons around these problem introns have no support in the final merged gff file, but a few are supported by blast hits. Is there a reason why these introns would remain in the final gff?
>  
> Thanks,
> Shawn 
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