[mira_talk] Re: Parsing SSAHA output with Mira 2.9.35x1

Hi Bastein:

Thanks for the advice.

Greg


Gregory P. Harhay, PhD
Computational Biologist
Animal Health Research Unit
USDA-ARS-Roman L. Hruska  U.S. Meat Animal Research Center
Clay Center, NE 68933
v - 402.762.4250




> From: Bastien Chevreux <bach@xxxxxxxxxxxx>
> Organization: Speaking for myself, really!
> Reply-To: <mira_talk@xxxxxxxxxxxxx>
> Date: Fri, 5 Dec 2008 23:20:48 +0100
> To: <mira_talk@xxxxxxxxxxxxx>
> Subject: [mira_talk] Re: Parsing SSAHA output with Mira 2.9.35x1
> 
> On Friday 05 December 2008 21:35, Gregory Harhay wrote:
>> Hi Bastien:
>> [...]
>> Is another way to check to see if the ssaha clips are actually getting into
>> mira? 
> 
> In a separate directory, assemble the three identical artificial sequences in
> the attachement with
> 
> mira -project=sal_BM -job=denovo,est,accurate,454 -fasta -notraceinfo
> -noclipping 
> 454_SETTINGS -CL:msvs=yes > & log.txt
> 
> then look up the resulting consensus. The clips given in the SSAHA file (and
> represented in lower case in the sequences) are gone.
> 
> 
>> The reason why I discovered the bug is because I'm generating many megahubs
>> that don't go away when I apply the ssaha clips.
> 
> Have a look at http://www.freelists.org/post/mira_talk/mmhr-problem,1 where
> the lower part of the mail gives a rough idea on how to find out what is
> wreaking havoc. I need to smooth out the whole thing, but it should give you
> an idea.
> 
> Looking at the fact that you are assembling ESTs (a non-normalised
> library?) ... I'd guess that some housekeeping genes may give you some
> headache.
> 
> Regards,
>   Bastien


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