[mira_talk] Re: How does Mira determine quality scores?

  • From: Davide Sassera <davide.sassera@xxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Mon, 03 Aug 2009 10:17:24 +0200

I tried an assembly and I saw no difference, but Bastien already found out why
To answer your question on where I get this problem: it's in gap4, which is my choice for checking the assembly
I attach a screenshot. you can also see in the screenshot that the quality of the highlighted gap is 1 (same for all gaps). Due to high coverage you cannot see all the reads but take my word, gaps are the vast majority.
As ready I am to help solve this problem I have to let you know I'm a newbie in bioinformatics, so maybe I'm just doing something wrong... I just do not know what 

D.



On Samstag 01 August 2009 Lionel Guy wrote:

That would be perfect... we could run 3-4 assemblies with different
thresholds and see which one is best !


Hello Guy, David,
as I just answered to Davide, I should have looked up my code more throroughly before answering. The changes I made were actually not-working as they were always true (a 66% majority is always also at least a 51% majority). So, there will be no special version as this would always give the same result anyway. 

Sorry for the confusion.

Just go on with your analysis regarding homopolymers as you planned to do.
On the upside, I re-activated this week-end TCS output where TCS stands for Transpose Contig Summary. It's the kind of file that might make your life easier if you want to evaluate things with a script. If you're interested to see what it provides: 

  http://www.chevreux.org/tmp/mira_3rc1b2_dev_linux-gnu_x86_64_static.tar.bz2

Then you can simply use
  convert_project -f caf -t tcs -r c input.caf ouputfile
to create the TCS from an existing CAF file.

Hope this helps,
  Bastien





--
Davide Sassera
Sezione di Patologia Generale e Parassitologia
Dipartimento di Patologia Animale, Igiene e Sanita` Pubblica Veterinaria Facolta` di Veterinaria 
Universita` degli Studi di Milano
Via Celoria 10, 20133, Milano, ITALY
Tel: +39 0250318094
Fax: +39 0250318095

PNG image

Other related posts:

  1. Home
  2. mira_talk
  3. Archive
  4. 08-2009