[mira_talk] Fwd: ace file output from MIRA

Many thanks for the fix as to how to load a MIRA ace file into consed. It works very well.
I would also be interested in finding ways to incorporate things like quality scores when reading MIRA output into consed. 

Regards,

Craig
we are also using consed to view MIRA outputs, and it is working fine in principle, although there have been a number of small errors. We are still not quite sure on why they happen. It also seems to be somewhat unpredictable; for some assemblies we get errors and for others not, and we can not quite tell yet what the differences are. We are happy to try to help working a bit on this to see if we can improve things, and we will let you know how we progress; the basic problem is that the consed support is not always great, and we've found 
it hard to find proper definitions of the file formats.


Now to the question:
Consed is designed to take an .ace file as input, but it also expects that there is a .phd-file for each read. (It is also possible to concatenate all 
.phd files into a single file 'phd.ball'.)
The basic problem is that MIRA does not create the .phd files. To circumenvent 
this problem, you might try to change your run command to
consed -nophd -ace ./pdt_results/pdt_out.ace
The downside of not having any .phd files is that the quality values for each read are only stored in the .phd-files, and so these can not be viewed in 
consed. The quality values of the contigs are ok though.
We have been thinking of creating .phd files (or rather a phd.ball) directly from the MIRA input files, but there might be trouble with some of the clipping options, so maybe a wish would be for MIRA to output a full consed folder 
similar to what Newbler does?
Good luck, and hoping to continue this discussion to the benfit of all :) 
Björn Nystedt


--
Craig Marshall  craig.marshall@xxxxxxxxxxx
Biochemistry http://biochem.otago.ac.nz/staff/marshall/cmarshall.html
University of Otago     Phone +64 3 479 7570 Fax +64 3 479 7866

Other related posts: