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 > > -- > You have received this mail because you are subscribed to the mira_talk > mailing list. For information on how to subscribe or unsubscribe, please > visit http://www.chevreux.org/mira_mailinglists.html _________________________________________________________________ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2