[mira_talk] Re: (no subject)
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 23 Jul 2014 04:36:57 +0200 (CEST)
> On July 23, 2014 at 2:17 AM "Mendez Garcia, Celia" <cmendezg@xxxxxxxxxxxx>
> wrote:
> thanks. It worked by re-trying. 256 GB is the amount of memory I'm using.
>Just 1 CPU core...
MIRA worked with 256 threads, so somehow I'm a bit puzzled.
> Another tiny tiny thing: I'm mapping several genomes against a reference and
>always get just one contig.
> My supervisor asks how come. What should I reply to this, I mean, is this
> usual?
You did a "mapping" and not a de-novo assembly, therefore this is to be expected
(if your reference sequence has 1 contig that is). MIRA fills gaps in the
reference with Ns, you should be able to spot these stretches easily in the
results.
May I suggest that you contact your Bioinformatics support group at your
institute and ask them to give you an introduction into the difference of
de-novo and mapping and when to use what? This actually is quite important for
you to understand.
Best,
Bastien
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