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Karma is top secret. Shh!
Karma is top secret. Shh!
* Download
*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]
* Command line
*Command line
<pre>Usage:
<pre>
Usage:
karma88 create [options...]
karma88 create [options...]
karma88 map [options...] file1.fastq.gz [file2.fastq.gz]
karma88 map [options...] file1.fastq.gz [file2.fastq.gz]
karma88 check [options...]
karma88 check [options...]
karma88 test [options...]
karma88 test [options...]
-d -> debug
-d -> debug
-s [int] -> set random number seed [12345]
-s [int] -> set random number seed [12345]
Defaults:
Defaults:
</pre>
</pre>
*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:
{| style="width: 445px; height: 150px" border="1" cellspacing="1" cellpadding="1" width="445"
|-
|
| Base Space
| Color pace
|-
| Reference genome
| NCBI37-bs.umfa
|
|-
| Word Index
|
NCBI37.umwihi
NCBI37.umwiwp
|
|-
| Word Hash (Left)
| NCBI37-bs15.umwhl
|
|-
| Word Hash (Right)
| NCBI37-bs15.umwhr
|
|}
<br>
basespace.umfa => NCBI36.bs.umfa
basespace.umfa => NCBI36.bs.umfa
colorspace.umfa => NCBI36.cs.umfa
colorspace.umfa => NCBI36.cs.umfa
colorspace.umwhr => NCBI36.cs.12.umwhr
colorspace.umwhr => NCBI36.cs.12.umwhr
colorspace.umwhl => NCBI36.cs.12.umwhl
colorspace.umwhl => NCBI36.cs.12.umwhl
colorspace.umwihi => NCBI36.cs.12.umwihi
colorspace.umwihi => NCBI36.cs.12.umwihi
colorspace.umwiwp => NCBI36.cs.12.umwiwp
colorspace.umwiwp => NCBI36.cs.12.umwiwp
* Other useful links:
*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]
[http://lh3lh3.users.sourceforge.net/bioinfo.shtml Heng Li's thoughts about aligner]
[http://lh3lh3.users.sourceforge.net/bioinfo.shtml Heng Li's thoughts about aligner]
[http://lh3lh3.users.sourceforge.net/udb.shtml Benchmark of Dictionary Structures]
[http://lh3lh3.users.sourceforge.net/udb.shtml Benchmark of Dictionary Structures]
