[mira_talk] Re: RE Re: batch processing multiple assembly jobs
- From: "He, Ji" <jhe@xxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Tue, 2 Mar 2010 15:09:15 -0600
RE: > While writting this e-mail, i'm thinking that in the mean time it would be
> good if you could document which options are affected by the quick
> switches,
> so that one can quickly spot which options to turn off if needed.
You'd get pretty crazy seeing the output. Furthermore, the things are in
change over time as I sometimes adapt to new situations. The way it works a
the moment is a whole cascade of rules adding to one another or overwriting
parameters set earlier. However, you can easily do this by changing one line
in the code.
----
I think what Jorge initially asked was if there is any form of "feature
comparison" for different working modes of MIRA, e.g. in EST mode, what
algorithms / functions are automatically turned on, what are the default
settings for some of the parameters, and how they differ from those in genome
mode or mapping mode, etc. I'd second that suggestion as I think it would
greatly help your users.
- Ji
-----Original Message-----
From: mira_talk-bounce@xxxxxxxxxxxxx [mailto:mira_talk-bounce@xxxxxxxxxxxxx] On
Behalf Of Bastien Chevreux
Sent: Tuesday, March 02, 2010 2:10 PM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: RE Re: batch processing multiple assembly jobs
On Dienstag 02 März 2010 Jorge.DUARTE@xxxxxxxxxxxx wrote:
> I'm myself working on high eukaryots, but I'd also like to have an option
> in between est and genome for assembling plant genomic gene rich data...
Wouldn't
--job=genome -SK:mnr=yes:nrr=10:mhpr=50
allow do get you going?
> Indeed, i think some options used in est assemblies could be usefull for
> assembling this type of data,
> but not all as we talk about genomic data, with introns ! But i find it
> difficult to figure out wich options to use and not use...
>
> Bastien, if you could add such an option for denovo and mapping
> assemblies, that would be great !!
Ummm ... is mapping a problem? It's "the easiest" part (I think) as it needs
to track only minimal info for repeats.
> While writting this e-mail, i'm thinking that in the mean time it would be
> good if you could document which options are affected by the quick
> switches,
> so that one can quickly spot which options to turn off if needed.
You'd get pretty crazy seeing the output. Furthermore, the things are in
change over time as I sometimes adapt to new situations. The way it works a
the moment is a whole cascade of rules adding to one another or overwriting
parameters set earlier. However, you can easily do this by changing one line
in the code.
In <src/mira/parameters.C>,
function <void MIRAParameters::parseQuickmode(...)>
theres a line commented out:
// verbose=true;
Remove the two slashes, recompile. But I warned you ... it is a nightmare to
follow. It might be easier to follow by looking at the logic in function <void
MIRAParameters::interpretJobDefs(...)>
Regards,
Bastien
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