[maker-devel] Advice on params for ciliates

[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


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

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