[mira_talk] Re: denovo results clarifications
- From: Stefano Ghignone <stefano.ghignone@xxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 29 Mar 2010 16:06:01 +0200
Hi Bastien,
On 03/28/2010 05:30 PM, Bastien Chevreux wrote:
Would the reads you have shown perhaps be very, very low coverage?
hmm. Let me tell about this fragment. As I told you, I originally got a
contig named *_lcr**, formed by 17 reads, about 700bp long. This contig
was assembled using phrap with 343 others *_lcr** and *_c** to form a
bigger contig of ~ 3000bp. The new contig ( contig of contig!! ) was
*perfect*; It also has been annotated and since we found an interesting
gene, we also did re-sequencing. so we also have sanger sequences of
that fragment. This happened last June, so I was using a v. 2.** of mira.
So I can say that this is absolutely not a very low coverage fragment.
"-CL:pec=no"
Tryed this morning, but nothing changed. It uses about 70000 454 reads
out of 389000.
I used this command:
mira -project=CaGgdn -job=denovo,genome,accurate,sanger,454
SANGER_SETTINGS -LR:mxti=no -CL:qc=yes -ED:ace=yes 454_SETTINGS
-LR:mxti=yes -CL:pvlc=yes:qc=yes:bsqc=yes -ED:ace=yes COMMON_SETTINGS
-CL:pec=no -SK:not=4 -OUT:ora=yes
which perhaps produces the same results of this:
mira -project=CaGgdn -job=denovo,genome,accurate,sanger,454
SANGER_SETTINGS -LR:mxti=no -CL:qc=yes:qcmq=18 -ED:ace=yes 454_SETTINGS
-LR:mxti=yes -ED:ace=yes COMMON_SETTINGS -AS:urd=no:sd=yes -OUT:ora=yes
Please note that I also switched off -AS:urd.
Would it be possible to get the data to see why MIRA fails on these?
Sure. I'll share with you data privately.
regards
stefano
--
Dr. Stefano Ghignone
Istituto per la Protezione delle Piante, Sez. Torino - CNR
c/o Dpt. Plant Biology, University of Turin
V.le P.A. Mattioli, 25
I-10125 Turin
Italy
Phone: +39 011 6502927 ext. 48
Fax: +39 011 6705962
e-mail: stefano.ghignone@xxxxxxxx
MSN: ste.ghi@xxxxxxxxxxx
http://www.bioveg.unito.it
http://www.sppadbase.com
http://www.dinamycode.it/
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