[mira_talk] convert_project, again
- From: Stefano Ghignone <stefano.ghignone@xxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 01 Dec 2009 17:55:53 +0100
Hi everybody,
I went through the mailing list archive searching for information about
the convert_project usage, but I didn't find any that fits my case. So
sorry if I treat again convert_project.
After the assembly step (which was actually a mapping, made with MIRA
v.2.9.37) of my hybrid Sanger/454 data, I checked that I was able to
successfully get a 4x filter on contigs using convert_project. I also
obtained the same output from MIRA as ACE file (since I use consed for
editing).
Now, after having DEEPLY edited the ace file with consed, I wanted to
apply again the 4x coverage filter, but I found out that convert_project
works only on CAF file. OK. So, I got from sanger institute the
phrap2caf script, which is supposed to convert an ace-file output to the
CAF format.
Unfortunately, the CAF output layout from phrap2caf is different from
the CAF layout produced by MIRA, and the convert_project doesn't work on it.
Is there anyone aware of a good tool to convert an ACE file to a CAF
file suitable to convert_project?
thanks a lot for your kind attention.
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
http://www.bioveg.unito.it
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -
--
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:
- » [mira_talk] convert_project, again - Stefano Ghignone
