[mira_talk] Re: 454 mapping

You could also use this:

[backbone_basequality(bbq)=*-1 ≤ integer ≤ 100*]

Default is -1. Defines the default quality that the backbone sequences have
if they came without quality values in their files (like in GBF format or
when FASTA is used without .qual files). A value of -1 mira to use the same
default quality for backbones as for reads.


Regards,

Juan Montenegro

2012/5/3 davis gimode <dgimode@xxxxxxxxx>

> Thanks a lot. Will give it a try.
>
> On Thu, May 3, 2012 at 2:57 PM, Isabelle Lesur
> <isabelle.lesur.kupin@xxxxxxxxx> wrote:
> > Hello!
> >
> > I used this parameter with 454 and Sanger sequences:
> > -AS:epoq=no
> > You can give it a try...
> >
> > MIRA manual says:
> >
> > [enforce_presence_of_
> > qualities(epoq)=on|yes|1, off|no|0] Default is yes. When set to yes, MIRA
> > will stop the assem-
> > bly if any read has no quality values loaded.
> >
> > However, I think your 454 sequences quality data will be ignored as
> well..
> >
> > Isabelle
> >
> >
> > 2012/5/3 davis gimode <dgimode@xxxxxxxxx>
> >>
> >> Hi,
> >> I am trying to do a mapping assembly of 454 data on to a reference
> >> genome. My call parameters are:
> >>
> >> mira --project=indica --job=mapping,genome,accurate,454 -AS:nop=4
> >>
> >>
> -SB:load_backbone=yes:startbackboneusage_inpass=3:backbone_strainname=indica_backbone_in.fasta:backbone_filetype=fasta:bbq=-1
> >>
> >> However, it requires quality  scores for the backbone i.e it wants
> >> indica_backbone_in.fasta.qual which i dont have. How do i disable mira
> >> from requiring the quality files?
> >>
> >> Thanks in advance
> >>
> >> --
> >> Davis M. Gimode
> >>
> >> --
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> >
> >
>
>
>
> --
> Davis M. Gimode
>
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