[mira_talk] Re: Question about turn off end clip.
- From: "Yi Zheng" <yz357@xxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 23 Nov 2009 16:48:59 -0500 (EST)
Hi Bastien,
The log info is too long so I post it on my blog :
http://kentnf.blogspot.com/2009/11/to-bastien-mira-log.html
> 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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