[maker-devel] Help: min_contig length

[Carson Holt]

There will be no negative effects in restarting.  The min_contig option just
speeds things up by skipping contigs that are likely too small to accurately
annotate.  Gene predictors generally require a certain amount of sequence
upstream and downstream of a gene to work accurately, so for most Eukaryotic
organisms, contigs of size of less than 10,000 will not produce results, but
if the genes are smaller in your organism you can reduce this.  The basic
idea is to just skip contigs that won't produce results anyways.

Thanks,
Carson



From:  Diego Calderon <dcalderon at wesleyan.edu>
Date:  Monday, 9 July, 2012 7:20 PM
To:  李青 Li, Qing <liqing850104 at gmail.com>
Cc:  Carson Holt <carsonhh at gmail.com>
Subject:  Re: Help: min_contig length

Just a little add on:
If we stop the currently running mpi maker, change the option from the
default 1 to 500 or 1000, then restart maker, will it have any (negative)
effect on maker (for example having to restart the analysis or something)?

I'm guessing that it will not, but we just wanted to make sure.

Best,
Diego


On Mon, Jul 9, 2012 at 5:11 PM, 李青 Li, Qing <liqing850104 at gmail.com>
wrote:
> Hi Carson,
> Very sorry for disturbing you! Diego and I are running maker for whole genome
> annotation now, and we have a question: should the min_contig=500 or 1000? We
> asked several people but get different answers,,, So we think you may be the
> best one to ask,,,
> Thank you!
> Best,
> Qing



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