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 | + | *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:
