[mira_talk] Re: Excessive coverage in 454: how to deal with it?
- From: Leonor Palmeira <mlpalmeira@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 18 Jun 2012 14:00:11 +0200
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On 18/06/12 12:03, Bastien Chevreux wrote:
> You expect ~120kb, MIRA thinks that the large contigs (13) toal 137 kB. Not
> too
> bad, especially considering it is a virus and that it is 454. So, the
> question I
> have is why you insist on looking at contigs MIRA categorised as junk :-)
The answer is simple: I just want to get the best out of this data :-)
More precisely, I was wondering how the reads in the 'contigs
categorised as junk' affect the assembly process:
- - can some of these reads be responsible for splitting contigs because
of ambiguities?
- - is this just sequencing errors and small repeats that cannot be
assembled in the larger contigs?
- - could this data still be interesting for my assembly?
- - is this contaminant data? if so, wouldn't it be best to filter this
out before the assembly process?
Thanks for your help,
Leonor.
> Please have a look at chapter "10. Working with the results of MIRA"
>
> http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#chap_results
> <http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#chap_results>
> and especially at section "10.2. First look: the assembly info"
>
> http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_first_look:_the_assembly_info
> <http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_first_look:_the_assembly_info>
> and section "10.4. Filtering results"
>
> http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_res_filtering_of_results
> <http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_res_filtering_of_results>
>
>
>
> B.
>
>
- --
Leonor Palmeira, PhD
Phone: +32 4 366 42 69
Email: mlpalmeira AT ulg DOT ac DOT be
http://sites.google.com/site/leonorpalmeira
Immunology-Vaccinology, Bat. B43b
Faculty of Veterinary Medicine
Boulevard de Colonster, 20
University of Liege, B-4000 Liege (Sart-Tilman)
Belgium
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