Difference between revisions of "Karma"
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* Command line | * Command line | ||
| + | <pre> | ||
| + | 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) | ||
| + | |||
| + | </pre> | ||
* File strucutre | * File strucutre | ||
Revision as of 23:53, 23 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:
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:
