[mira_talk] Re: Bivalve EST assembling

  • From: Juan Fernandez Tajes <jfernandezt@xxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 13 Oct 2011 00:26:17 +0200

Thanks Bastien for your quick replay

Here are the hash statistics

Hash statistics:
=========================================================
Measured avg. frequency coverage: 7

Deduced thresholds:
-------------------
Min normal cov: 3
Max normal cov: 11
Repeat cov: 13
Heavy cov: 56
Crazy cov: 140
Mask cov: 70

Repeat ratio histogram:
-----------------------
0       9869618
1       5691550
2       1024738
3       383504
4       188150
5       111226
6       71370
7       49218
8       37936
9       28164

I only paste the first 9 lines from repeat ratio histogram, if you need
more let me know

Juan

El mié, 12-10-2011 a las 20:38 +0200, Bastien Chevreux escribió:
> On Wednesday 12 October 2011 19:08:55 Juan Fernandez Tajes wrote:
> 
> > I got Mira to work but I had to increase, mmhr=3, I hope I didn't do
> 
> > anything wrong, although Bastien warn in manual about modifying
> mmhr.
> 
> > The problem is after Mira has finished I got a number of all contigs
> too
> 
> > high, All contigs=34276 contigs, and I think this number is too much
> for
> 
> > 250641 reads assembled, any clues about what is happening?
> 
> 
> You've got some massive repeats. Being EST data, my first guess would
> be rRNA, but that you'd need to check.
> 
> 
> Let's walk this through.
> 
> 
> Can you please post the hash statistics shown in the log output?
> 
> 
> B.
> 
> 



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