[mira_talk] Re: tweaking Manifest for polyploid genome
- From: Hanquan Liang <hliang@xxxxxxx>
- To: mira_talk <mira_talk@xxxxxxxxxxxxx>
- Date: Sun, 23 Feb 2014 23:06:33 -0600
I'm encountering a similar problem in a fungus project. But it's genome
assembly, not transcriptome. I tried *default* settings and the assembly is
twice as big as expected.
I suspect mira separated two haploids and builded contigs for each.
Blasting with genes from a closely related species supports this idea. Each
gene has hits on two contigs, with similar alignment length and high scores.
Bastien, which mira parameters do you recommend exploring if one wants to
separate (or merge) different genomes of polyploid, better?
Currently in my list: -SK:pr, -AL:mrs, -AL:ms.
Hanquan
On Sun, Feb 23, 2014 at 8:07 AM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On 22 Feb 2014, at 20:55 , Gutierrez, Juan <Juan.Gutierrez@xxxxxxxxxxxx>
> wrote:
>
> I am trying to do RNA-seq de novo on a polyploid (hexaploid) genome using
> a combination of 454 and illumina 100bp paired ended reads. The three
> copies of each gene are highly similar to one another.
>
>
> Care to expand a bit more on the "highly similar" criterion? Is it one
> diff per 100bp, per 1000bp, per 10000bp, ...?
>
> B.
>
>
>
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