[mira_talk] Re: About ends clipping

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

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