Difference between revisions of "Karma"
From Genome Analysis Wiki
Jump to navigationJump to search| Line 20: | Line 20: | ||
seed 12345 (default 12345) | seed 12345 (default 12345) | ||
| − | </pre> | + | </pre> |
*File strucutre | *File strucutre | ||
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| − | Base | + | Base Space |
| − | |||
| − | |||
| − | |||
| + | | Color Space | ||
|- | |- | ||
| | | | ||
| − | Reference genome | + | Reference genome |
| | | | ||
| − | NCBI37-bs.umfa | + | NCBI37-bs.umfa |
| + | | NCBI37-cs.umfa | ||
|- | |- | ||
| | | | ||
| − | Word Index | + | Word Index |
| | | | ||
| − | NCBI37-bs.15.5000.umwiwp NCBI37-bs.15.5000.umwihi | + | NCBI37-bs.15.5000.umwiwp NCBI37-bs.15.5000.umwihi |
| + | | NCBI37-cs.15.5000.umwiwp NCBI37-cs.15.5000.umwihi<br> | ||
|- | |- | ||
| | | | ||
| − | Word Hash (Left) | + | Word Hash (Left) |
| | | | ||
| − | NCBI37-bs.15.5000.umwhl | + | NCBI37-bs.15.5000.umwhl |
| + | | NCBI37-cs.15.5000.umwhl | ||
|- | |- | ||
| | | | ||
| − | Word Hash (Right) | + | Word Hash (Right) |
| | | | ||
| − | NCBI37-bs.15.5000.umwhr | + | NCBI37-bs.15.5000.umwhr |
| − | | | + | | NCBI37-cs.15.5000.umwhr |
|} | |} | ||
| − | <br> | + | <br> |
basespace.umfa => NCBI36.bs.umfa | basespace.umfa => NCBI36.bs.umfa | ||
Revision as of 18:07, 29 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 |
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 |
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:
