[mira_talk] Re: 454 mapping
- From: davis gimode <dgimode@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 3 May 2012 16:21:48 +0300
Thanks Juan, thing is, I've used bbq=-1 still it wants the qual file..
thanks though
On Thu, May 3, 2012 at 3:52 PM, Juan Daniel Montenegro Cabrera
<jdmontenegroc@xxxxxxxxx> wrote:
> 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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>
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