[mira_talk] Re: scaffolded contigs

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


-- 
Dana Price
Laboratory Researcher in Bioinformatics
Rutgers, The State University
Bhattacharya Lab
http://dblab.rutgers.edu
d.price@xxxxxxxxxxx

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