[maker-devel] Advice on params for ciliates

[Bob Freeman]

Thanks, Carson, for these helpful hints.

(Separately, the other code did not work again on our cluster. Have been so swamped -- I'll get to the write-up next week. Have been using the 2.25beta binary and that works OK).

Best,
Bob

On Jun 3, 2013, at 9:04 AM, Carson Holt wrote:

> I don't have any specific advice, but In general I always set blast_depth parameters in the maker_bopts file to 20 or 30 (faster runtimes).  Also max_dna_len can be set to 2x higher if you have sufficient memory (3-4 Gb per cpu as opposed to 1-2 Gb that are assumed with the default).
> 
> Other than that split_hit, pred_flank, and single_exon are the only ones I might change around.  You sort of have to run on a few large contigs before deciding what to do with these parameters.
> 
> split_hit --> set max intron size for alignments
> pred_flank --> affects clustering for gene dense organisms
> single_exon --> leave off unless you expect a lot of singel exon genes.
> 
> --Carson
> 
> 
> From: "Freeman, Robert M." <Bob_Freeman at hms.harvard.edu>
> Date: Thursday, 23 May, 2013 4:17 PM
> To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Advice on params for ciliates
> 
> Dear MAKER community,
> 
> Am embarking on updating models for a ciliate (taxa Ciliophora) and was wondering if folks had recommendations for MAKER parameters. 
> 
> Thanks,
> Bob
> 
> 
> _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-----------------------------------------------------
Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2294, vox

"Sorry I'm late. Oh, God, that sounded insincere. I'm late."
	-- Karen Walker, from Will and Grace



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