[mira_talk] Re: [mira_talk] (无主题)
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 7 May 2015 21:17:43 +0200
On 06 May 2015, at 9:09 , machenyu <machenyu@xxxxxxxxx> wrote:
I am an researcher from China.Mira is a very powerful tool to do local
assembly.It helps a lot in my research.However,I still wonder how mira deals
with the low quality bases,I mean will mira select informative bases with a
specific cutoff(eg phred value>20) when doing assembly? I do not find any
info about this in the manual.Could you explain that to me? Thanks in advance!
There is a whole battery of clipping algorithms implemented in MIRA. The
quality based clipping you are thinking of is covered by -CL:qc (quality_clip)
and -CL:bsqc (bad_stretch_quality_clip), which are described in
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_ref_clipping_cl
and are both clippers based on a window and quality threshold.
However, they are both switched off by default. MIRA has a number of other
automatic clipping algorithms which perform way better than simple quality
based clips, which even improved once again drastically in the 4.9.x
development versions.
B.
--
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:
