[mira_talk] Re: About ends clipping
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 30 Apr 2009 20:23:28 +0200
On Tuesday 28 April 2009 Yi Zheng wrote:
> We are currently using mira to assemble cDNA (EST) sequences which should
> be low coverage of the transcriptome.
> If I switch off the -CL:pec as you recommended, we found that quite a few
> sequences not assembled together only differ in a short
> stretch of the ends (which are usually in relatively low quality). If I
> switch on, then the information of a lot of alternative
> splicing will be lost.
For these cases, the -CO:emea parameter might be what you're searching for.
Please give it a try (and please tell whether it succeeded for you or not).
The switch for this would not be too hard, but you couldn't really go below 12
anyway as then you'd very probably have too many false negatives. At the
moment I'm happy if I can get around building in YAS (Yet Another Switch) into
MIRA.
Regards,
Bastien
--
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:
