Difference between revisions of "Karma"
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Karma is top secret. Shh! | Karma is top secret. Shh! | ||
| − | + | = 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] | ||
| − | + | = Build Reference = | |
| − | + | ||
| + | == Options == | ||
| + | |||
| + | Command line | ||
| + | |||
| + | Usage: | ||
| + | |||
karma88 create [options...] | karma88 create [options...] | ||
| − | + | karma88 map [options...] file1.fastq.gz [file2.fastq.gz] | |
| − | Diagnostics: | + | |
| + | Diagnostics: | ||
| + | |||
karma88 check [options...] | karma88 check [options...] | ||
| − | + | karma88 test [options...] | |
| − | + | -d -> debug | |
| − | + | -s [int] -> set random number seed [12345] | |
| − | Defaults: | + | Defaults: |
| − | debug off (default off) | + | debug off (default off) seed 12345 (default 12345) |
| − | seed 12345 (default 12345) | ||
| − | + | == File structure == | |
| − | |||
| − | + | Upon successfully building references, you will obtain a list of reference files like below: | |
| − | |||
| − | |||
{| style="width: 571px; height: 288px" border="1" cellspacing="1" cellpadding="1" width="571" | {| style="width: 571px; height: 288px" border="1" cellspacing="1" cellpadding="1" width="571" | ||
| Line 47: | Line 51: | ||
| | | | ||
| − | 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 | ||
| − | |||
|- | |- | ||
| | | | ||
| Line 70: | Line 80: | ||
<br> | <br> | ||
| − | + | <br> | |
| − | + | ||
| − | + | = Align Illumina Reads = | |
| − | + | ||
| − | + | Command line: | |
| − | + | ||
| + | <pre> | ||
| + | karma map -r reference.fa read1.fastq read2.fastq -o output.sam | ||
| + | </pre> | ||
| + | |||
| + | = Align ABI SOLiD Reads = | ||
| + | |||
| + | Command line: | ||
| + | |||
| + | <pre> | ||
| + | karma map -r reference.fa -c read1.fastq read2.fastq -o output.sam | ||
| + | </pre> | ||
| + | |||
| − | + | = 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] | ||
Revision as of 17:36, 30 March 2010
Karma is top secret. Shh!
Download
To get a bootleg copy go to Karma Download
Build Reference
Options
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 structure
Upon successfully building references, you will obtain a list of reference files like below:
|
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 |
Align Illumina Reads
Command line:
karma map -r reference.fa read1.fastq read2.fastq -o output.sam
Align ABI SOLiD Reads
Command line:
karma map -r reference.fa -c read1.fastq read2.fastq -o output.sam
