[mira_talk] edited assembly: reassembly
- From: Stefano Ghignone <stefano.ghignone@xxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 11 Dec 2009 11:09:00 +0100
Hi all,
and sorry if I bother again the mailing list with my issues.
I need to reassemble an assembly (a mapping, precisely), which I edited
using consed, working on the ACE output.
My case matches the point 3 of "Using backbones to perform a mapping
assembly against a reference sequence" in the short usage manual:
Backbone sequences will not not be assembled together! That is, if a
sequence of the backbones has a perfect overlap with another backbone
sequence, the will still not be merged. So I did this manually. Now I
still have a lot of contigs, mainly made by 454 sequences, which are
clearly combinable together, but its impossible do it manually in a
reasonable frame of time. Since I worked on the ACE file, which could be
the right strategy to reassemble 454-contigs?
And I'm still trying to convert the ace file into the caf format. I was
thinking to reassemble with mira using the caf file as input, after
filtering out contig with less than 4x of coverage. I used phred2caf and
roche454ace2caf, but both produce a caf file which convert_project
doesn't like. With the latter script, by Bernd Senf, I got this message
when I apply convert_project:
Converting from caf to: caf
First counting reads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
....|.... [90%] ....|.... [100%]
Now loading and processing data:
[0%] Searched for read fos10Contig6.c but did not find it?
Unable to find Read in Pool
Internal logic/programming/debugging error (*sigh* this should not
have happened).
Please contact the author: bach@xxxxxxxxxxxx
"fos10Contig6.c"
->Thrown: Readname not found in hash as expected?
->Caught: int32 CAF::getCafAssembledFrom()
Program aborted.
Program aborted.
fos10Contig6.c is a sequence used as backbone, but actually it is
present in the caf file!
any suggestion is wellcome!
cheers
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
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -
--
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
Other related posts:
