[mira_talk] Re: scaffolded contigs
- From: "Davide Scaglione" <gianza@xxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 21 Jul 2010 14:49:35 +0200
Fourth!
From: Dana Price
Sent: Wednesday, July 21, 2010 2:38 PM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: scaffolded contigs
I third that request.. it would be an extremely useful feature.
On Wed, Jul 21, 2010 at 8:22 AM, Davide Sassera <davide.sassera@xxxxxxxx> wrote:
Wow, sounds great!
I join Adnan in the request, it would be sweet to have it
Davide
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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Davide Sassera
Sezione di Patologia Generale e Parassitologia
Dipartimento di Patologia Animale,
Igiene e Sanità Pubblica Veterinaria
Facoltà di Veterinaria
Università degli Studi di Milano
Via Celoria 10, 20133, Milano, ITALY
Tel: +39 0250318094
Fax: +39 0250318095
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Dana Price
Laboratory Researcher in Bioinformatics
Rutgers, The State University
Bhattacharya Lab
http://dblab.rutgers.edu
d.price@xxxxxxxxxxx
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