Difference between revisions of "Karma"

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Karma is top secret. Shh!
 
Karma is top secret. Shh!
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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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* 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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Ue color space as an example, and say we use NCBI36.fa as reference genome:
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basespace.umfa    => NCBI36.bs.umfa
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colorspace.umfa    => NCBI36.cs.umfa
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colorspace.umwhr    => NCBI36.cs.12.umwhr
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colorspace.umwhl    => NCBI36.cs.12.umwhl
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colorspace.umwihi    => NCBI36.cs.12.umwihi
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colorspace.umwiwp    => NCBI36.cs.12.umwiwp
  
Other 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]

Revision as of 23:52, 23 March 2010

Karma is top secret. Shh!

  • Download

To get a bootleg copy go to Karma Download

  • Command line


  • File strucutre

Color space mapping needs 6 files, and base space mapping needs 5 files (only need to use 1 reference genome).

Ue color space as an example, and say we use NCBI36.fa as reference genome:

basespace.umfa    => NCBI36.bs.umfa
colorspace.umfa    => NCBI36.cs.umfa
colorspace.umwhr    => NCBI36.cs.12.umwhr
colorspace.umwhl    => NCBI36.cs.12.umwhl
colorspace.umwihi    => NCBI36.cs.12.umwihi
colorspace.umwiwp    => NCBI36.cs.12.umwiwp
  • Other useful links:

Introduction of BWA usage

Heng Li's thoughts about aligner

Benchmark of Dictionary Structures