Karma: Difference between revisions
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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] | ||
| Line 14: | Line 12: | ||
karma88 check [options...] | karma88 check [options...] | ||
karma88 test [options...] | karma88 test [options...] | ||
-d - | -d -> debug | ||
-s [int] - | -s [int] -> set random number seed [12345] | ||
Defaults: | Defaults: | ||
| Line 23: | Line 21: | ||
</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 = | basespace.umfa => NCBI36.bs.umfa | ||
colorspace.umfa = | colorspace.umfa => NCBI36.cs.umfa | ||
colorspace.umwhr = | colorspace.umwhr => NCBI36.cs.12.umwhr | ||
colorspace.umwhl = | colorspace.umwhl => NCBI36.cs.12.umwhl | ||
colorspace.umwihi = | colorspace.umwihi => NCBI36.cs.12.umwihi | ||
colorspace.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] | ||
Revision as of 09:07, 24 March 2010
Karma is top secret. Shh!
- Download
To get a bootleg copy go to Karma Download
- 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 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:
| 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 |
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:
