[mira_talk] Re: Question about turn off end clip.
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 23 Nov 2009 22:14:34 +0100
On Montag 23 November 2009 Yi Zheng wrote:
> Hi Bastien,
>
> I have a end clip problem when using new 3rc4 version on 454 data.
>
> Below is my command:
> mira -project=est1 -job=denovo,est,normal,454 -fasta=est1.fa -notraceinfo
> -noclipping -GE:not=1:kcim=yes 454_SETTINGS -LR:wqf=no -AS:epoq=no:mrl=30
> COMMON_SETTINGS -AS:nop=4 -SK:not=1 -CL:pec=no 454_SETTINGS
> -CL:cpat=no:pvlc=no:qc=no:bsqc=no:mbc=no:emlc=no:emrc=no:llc=no:msvs=no
> -AL:mo=29:mrs=93
You turned off -CL:pec ... at least your command line says it. Can you please
post the first 2000 lines of the log?
> If possible, I want to know how to use '-CL:pec' and 'pecbph' to control
> the length of end clip when turn on it.
-CL:pecbh controls the length of kmers used to do the clipping, so it also is
the minimum amount which can be clipped. Please note that values <14 probably
don't make a lot of sense.
Use cautiously for EST assemblies anyway.
> For example, if a est's end was cliped more than 40bp, how to reject it
> from result.
Not possible, sorry. You can only filter for minimum read length.
Regards,
Bastien
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