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Karma (view source)

Revision as of 17:36, 30 March 2010

75 bytes removed ,  17:36, 30 March 2010
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Karma is top secret. Shh!  
 
Karma is top secret. Shh!  
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*Download
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= Download =
    
To get a bootleg copy go to [http://www.sph.umich.edu/csg/pha/karma/download/ Karma Download]  
 
To get a bootleg copy go to [http://www.sph.umich.edu/csg/pha/karma/download/ Karma Download]  
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*Command line
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= Build Reference  =
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<pre>Usage:
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== Options  ==
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Command line  
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Usage:  
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   karma88 create [options...]
 
   karma88 create [options...]
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  karma88 map [options...] file1.fastq.gz [file2.fastq.gz]
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karma88 map [options...] file1.fastq.gz [file2.fastq.gz]
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Diagnostics:
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Diagnostics:  
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   karma88 check [options...]
 
   karma88 check [options...]
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  karma88 test [options...]
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karma88 test [options...]
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  -d -&gt; debug
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-d -&gt; debug
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  -s [int] -&gt; set random number seed [12345]
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-s [int] -&gt; set random number seed [12345]
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Defaults:
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Defaults:  
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debug off (default off)
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debug off (default off) seed 12345 (default 12345)  
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seed 12345 (default 12345)
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</pre>
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== File structure  ==
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*File strucutre
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Color space mapping needs 6 files, and base space mapping needs 5 files (only need to use 1 reference genome).
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Upon successfully building references, you will obtain a list of reference files like below:  
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Ue color space as an example, and say we use NCBI36.fa as reference genome:  
      
{| style="width: 571px; height: 288px" border="1" cellspacing="1" cellpadding="1" width="571"
 
{| style="width: 571px; height: 288px" border="1" cellspacing="1" cellpadding="1" width="571"
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NCBI37-bs.15.5000.umwiwp NCBI37-bs.15.5000.umwihi  
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NCBI37-bs.15.5000.umwiwp  
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NCBI37-bs.15.5000.umwihi
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|
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NCBI37-cs.15.5000.umwiwp
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NCBI37-cs.15.5000.umwihi  
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| NCBI37-cs.15.5000.umwiwp NCBI37-cs.15.5000.umwihi<br>
   
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<br>  
 
<br>  
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basespace.umfa    =&gt; NCBI36.bs.umfa
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<br>
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colorspace.umfa    =&gt; NCBI36.cs.umfa
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colorspace.umwhr    =&gt; NCBI36.cs.12.umwhr
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= Align Illumina Reads =
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colorspace.umwhl    =&gt; NCBI36.cs.12.umwhl
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colorspace.umwihi    =&gt; NCBI36.cs.12.umwihi
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Command line:
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colorspace.umwiwp    =&gt; NCBI36.cs.12.umwiwp
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<pre>
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karma map -r reference.fa read1.fastq read2.fastq -o output.sam
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</pre>
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= Align ABI SOLiD Reads =
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Command line:
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<pre>
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karma map -r reference.fa -c read1.fastq read2.fastq -o output.sam
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</pre>
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*Other useful links:
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= Other useful links =
    
[http://www.broadinstitute.org/files/shared/mpg/nextgen2010/nextgen_li.pdf Introduction of BWA usage]  
 
[http://www.broadinstitute.org/files/shared/mpg/nextgen2010/nextgen_li.pdf Introduction of BWA usage]  
Zhanxw
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