Difference between revisions of "Karma"
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Ue color space as an example, and say we use NCBI36.fa as reference genome: | Ue color space as an example, and say we use NCBI36.fa as reference genome: | ||
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| − | | Base Space | + | | |
| − | | Color | + | Base Space |
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| + | Color Space | ||
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| + | Reference genome | ||
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| + | NCBI37-bs.umfa | ||
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| − | NCBI37.umwihi | + | Word Index |
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| + | NCBI37-bs.15.5000.umwiwp NCBI37-bs.15.5000.umwihi | ||
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| + | Word Hash (Left) | ||
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| + | NCBI37-bs.15.5000.umwhl | ||
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| − | + | Word Hash (Right) | |
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| − | | NCBI37- | + | | |
| + | NCBI37-bs.15.5000.umwhr | ||
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|} | |} | ||
Revision as of 13:53, 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 Space | |
|
Reference genome |
NCBI37-bs.umfa | |
|
Word Index |
NCBI37-bs.15.5000.umwiwp NCBI37-bs.15.5000.umwihi | |
|
Word Hash (Left) |
NCBI37-bs.15.5000.umwhl | |
|
Word Hash (Right) |
NCBI37-bs.15.5000.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:
