[mira_talk] Re: some questions

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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