[maker-devel] Advice on params for ciliates

[Freeman, Robert M.]

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

-----------------------------------------------------

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

[Carson Holt]

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

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[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_F...@hms.harvard.edu>
Date: Thursday, 23 May, 2013 4:17 PM
To: "maker...@yandell-lab.org" <maker...@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

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