[mira_talk] Re: Where is my assembly at?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 25 Sep 2011 16:21:25 +0200
On Sunday 25 September 2011 15:55:48 Visam Gültekin wrote:
> Thank you for rapid reply. With comparison to newbler and celera, mira is
> the absolute winner ( for data i have).
Well, always good to hear that.
> It is completely off the topic, but what if i have some EST sequences that
> i do not know which technology has been used for sequencing(Sanger-454..),
>
> i did some test with mira --job=est,.. for Sanger and 454 independently.
> There seems to be no difference b/w results. Any suggestions?
For that, you really should open a new thread so that one does not loose track
of what a discussion is all about.
That being said ... depending on the data it is possible, although not very
likely. MIRA has a couple of different rules for Sanger and 454. E.g., for
Sanger it will by default set SNPs or repeat markers also for gap vs no-gap
situations whereas for 454 this is switched off by default.
Are you sure the results are 100% identical? Or are they just similar?
One way to test that is to use only one thread to do the assembly
("-GE:not=1") in each case, then the result files should be 100% identical.
Best,
Bastien
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