Difference between revisions of "Karma"

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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
+
= Build Reference  =
<pre>Usage:
+
 
 +
== Options  ==
 +
 
 +
Command line  
 +
 
 +
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]
Diagnostics:
+
 
 +
Diagnostics:  
 +
 
 
   karma88 check [options...]
 
   karma88 check [options...]
  karma88 test [options...]
+
karma88 test [options...]
  -d -&gt; debug
+
-d -&gt; debug
  -s [int] -&gt; set random number seed [12345]
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-s [int] -&gt; set random number seed [12345]
  
Defaults:
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Defaults:  
  
debug off (default off)
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debug off (default off) seed 12345 (default 12345)  
seed 12345 (default 12345)
 
  
</pre>
+
== File structure  ==
*File strucutre
 
  
Color space mapping needs 6 files, and base space mapping needs 5 files (only need to use 1 reference genome).
+
Upon successfully building references, you will obtain a list of reference files like below:  
 
 
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  
 +
 
 +
NCBI37-bs.15.5000.umwihi
 +
 
 +
|
 +
NCBI37-cs.15.5000.umwiwp
 +
 
 +
NCBI37-cs.15.5000.umwihi  
  
| NCBI37-cs.15.5000.umwiwp NCBI37-cs.15.5000.umwihi<br>
 
 
|-
 
|-
 
|  
 
|  
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<br>  
 
<br>  
  
basespace.umfa    =&gt; NCBI36.bs.umfa
+
<br>
colorspace.umfa    =&gt; NCBI36.cs.umfa
+
 
colorspace.umwhr    =&gt; NCBI36.cs.12.umwhr
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= Align Illumina Reads =
colorspace.umwhl    =&gt; NCBI36.cs.12.umwhl
+
 
colorspace.umwihi    =&gt; NCBI36.cs.12.umwihi
+
Command line:
colorspace.umwiwp    =&gt; NCBI36.cs.12.umwiwp
+
 
 +
<pre>
 +
karma map -r reference.fa read1.fastq read2.fastq -o output.sam
 +
</pre>
 +
 
 +
= Align ABI SOLiD Reads =
 +
 
 +
Command line:
 +
 
 +
<pre>
 +
karma map -r reference.fa -c read1.fastq read2.fastq -o output.sam
 +
</pre>
 +
 
  
*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]  

Revision as of 17:36, 30 March 2010

Karma is top secret. Shh!

Download

To get a bootleg copy go to Karma Download

Build Reference

Options

Command line

Usage:

  karma88 create [options...]
karma88 map [options...] file1.fastq.gz [file2.fastq.gz]

Diagnostics:

  karma88 check [options...]
karma88 test [options...]
-d -> debug
-s [int] -> set random number seed [12345]

Defaults:

debug off (default off) seed 12345 (default 12345)

File structure

Upon successfully building references, you will obtain a list of reference files like below:

Base Space

Color Space

Reference genome

NCBI37-bs.umfa

NCBI37-cs.umfa

Word Index

NCBI37-bs.15.5000.umwiwp

NCBI37-bs.15.5000.umwihi

NCBI37-cs.15.5000.umwiwp

NCBI37-cs.15.5000.umwihi

Word Hash (Left)

NCBI37-bs.15.5000.umwhl

NCBI37-cs.15.5000.umwhl

Word Hash (Right)

NCBI37-bs.15.5000.umwhr

NCBI37-cs.15.5000.umwhr



Align Illumina Reads

Command line:

karma map -r reference.fa read1.fastq read2.fastq -o output.sam

Align ABI SOLiD Reads

Command line:

karma map -r reference.fa -c read1.fastq read2.fastq -o output.sam


Other useful links

Introduction of BWA usage

Heng Li's thoughts about aligner

Benchmark of Dictionary Structures