[mira_talk] Re: assembly options for non-redundant contigs
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 4 Jun 2009 23:55:59 +0200
On Mittwoch 03 Juni 2009 Richard Gregory wrote:
> The "good" results were from V2.9.15 . Making sure this effect was real,
> I've just tried assembling an old dataset using 2.9.43 and exactly the
> same input reads. This example uses pre-Titanium reads, a pool of two
> samples of relatively degraded cdna with an average read length 120bp.
> [...]
Hmmm ... 2.9.15 is from one and a half years ago. A lot has changed in the
mean time and I'll need to investigate that.
The question is: why does MIRA put things apart that it now thinks do not
belong together. One idea I have is (as I changed poly-A/T clip handling) that
it now sses more "differences" in these parts and therefore has the effect you
noticed.
In the end, it would be best if this could be looked at with some very specific
examples at hand. Would it be possible for you to make available for me one of
these data sets? If yes, you could show me a few cases that trouble you and I
would have a deeper look at what happened (or did not happen).
Regards,
Bastien
PS: Please note that this could probably only happen mid to end of next week
or later as I this week-end is already reserved for something else and then
I'm on travel.
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
