[mira_talk] Re: some questions

thank you so much for this help Bastien,
just a question:
Do you see something wrong or not good in my command line below:
mira -project=ESTUR -job=denovo,est,normal,454 -SK:mnr=yes -SK:rt=4 -GE:not=2 -CO:asir=yes -CO:mr 454_SETTINGS -AL:mrs=95:egp=yes:egpl=reject_codongaps:megpp=100 -CO:rodirs=10 -AL:mo=60 -CL:cpat 

(i work with titanium 454 reads)

Laurent --




Bastien Chevreux a écrit :

On Mittwoch 06 Mai 2009 Laurent MANCHON wrote:

do you think it's necessary to use parameter -CL:cpat with 454 titanium
reads ?
-CL:cpat should be used for all kinds of EST reads, regardless of the technology (Sanger, 454 etc.). Be careful: do not clip twice! (more on that in one of the manuals, I just can't remember which one at the moment). 


Why the sequences in padded file results are in lower case ? is there an
option to put them in upper case ?


Running the result file through a 'tr' should do the trick.


I have use the option -OUT:sssip to keep out debris files but it doesn't
work, the debris files are not stored in the results directory.
Not? Hmmm, they should. I'll need to investigate. Anyway, I recommend not using -OUT:sssip for larger datasets (that slows down MIRA quite a lot in the end-game ... setting up contig structures just for a singlet is quite time intensive). Instead, if you really want these singlets / debris / whatever, append them to the result file when you need. 

Regards,
  Bastien

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