[mira_talk] Re: scaffolded contigs

Thanks for reply and great work. Can i get that?

Regards
/adnan
 




> Date: Wed, 21 Jul 2010 11:40:24 +0100
> Subject: [mira_talk] Re: scaffolded contigs
> From: peter@xxxxxxxxxxxxxxxxxxxxx
> To: mira_talk@xxxxxxxxxxxxx
> 
> On Wed, Jul 21, 2010 at 11:27 AM, Adnan Niazi <niazi84@xxxxxxxxxxx> wrote:
> > Hi all,
> > Can anyone tell me is it possible to get scaffolded contigs in MIRA mapping.
> > I mean after mapping reads with reference sequence, some regions little or
> > no coverage. But when i view both padded and unpadded consensus fasta file,
> > the contig before zero coverage region and contig after zero coverage is
> > joined with reference sequence. I dont want bp of reference sequence to be
> > added in the fasta file. Is there some way i can insert NNNNN or *****
> > between those contigs? Hope i cleared my problem.
> >
> > Regards
> > /adnan
> 
> Hi Adnan,
> 
> I think I understand your question. I needed to do something similar recently
> and wrote a python script to parse the ACE file, and where the coverage was
> below a certain level I replaced the consensus letter with an N. This gave me
> a scaffold based on the reference with only the regions supported by read data
> present as ACGT, and the unsupported regions as N.
> 
> Peter
> 
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