[maker-devel] Long introns from Augustus

[Shane Brubaker]

Actually these are calls directly from Augustus (without using Maker).  They are not purely ab initio in that they are using hints from RNA-Seq data.

I had noticed that Maker does have some information about max intron length - does that mean it could be taken care of by Maker?  I don't have very good "EST" (transcriptome) assemblies because it is a very difficult organism to sequence.


-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Thursday, March 06, 2014 3:47 PM
To: Shane Brubaker; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] Long introns from Augustus

Are these the ab intio calls that are merged or final MAKER models.

—Carson


On 3/6/14, 4:41 PM, "Shane Brubaker" <sbrubaker at solazyme.com> wrote:

>Hi, we have a very compact genome and we are getting a lot of fused 
>gene models from running Augustus.  I am wondering if anyone has any 
>advice about how to prevent introns above a certain cutoff from being created?
>
>I tried a couple of things, some settings in a probabilities file and 
>also changing a long list of probabilities to another file that someone 
>had suggested on a forum.  So far I don't really see any changes though.
>
>Any advice would be greatly appreciated.
>
>Thanks,
>Shane
>
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