[mira_talk] Re: Pooled Multiple Strain Strategy
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 14 Mar 2011 17:19:49 +0100
On Monday 14 March 2011 16:51:58 Robin Kramer wrote:
> I won't name names, but I keep getting requests to do "pooled" est analysis
> with dozens strains of tetraploid organisms in one run of mira without
> using the individual strain settings.
*urglks* tetraploid _and_ multiple strains ... this is going to hurt.
> I believe strongly that this is not the right way to do that, but I would
> like to ask your opinion.
In general I would agree: giving strain information to MIRA might help to
alleviate a bit the problem posed by genuine differences. So, if possible, one
should design experiments accordingly.
But, and it's an important but, everything is relative. It depends on the
question one has to the data set. For specific cases, like, e.g., if you are
hunting some very specific genes at low relative expression, it is absolutely
possible that pooling the samples gets you much better chances of finding and
assembling your target.
As I wrote: in general though I'd be very, very cautious to even touch such a
data set.
Best,
Bastien
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