[mira_talk] Re: About ends clipping
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 25 Apr 2009 12:29:30 +0200
On Thursday 23 April 2009 Yi Zheng wrote:
> I download 2.9.44 version, use -CL:pec=yes to clip the ends of sequence,
> but the clipping part is too long, I want set the clipping length lower
> than 15bp.
> How to set it for just clip a part of ends?
Hello Yi,
the -CL:pec is currently tied to a hash analysis which is in turn tied to -
SK:bph. I would recommend not to try and get values much lower than 15. MIRA
uses the clean ends to help dissociate different repeats from each other.
May I ask why you want to reduce this length? For high coverage data (as you
typically get with 454 or Solexa), the probability that you lose a weak contig
join or some important coverage data is really, really small. And in low
coverage projects I would recommend to switch off -CL:pec anyway as there it
really hurts.
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:
