Karma
From Genome Analysis Wiki
Revision as of 16:53, 7 April 2010 by Pha (talk | contribs) (→Align Illumina Reads: fix argument order)
The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.
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 -o output.sam read1.fastq read2.fastq
Align ABI SOLiD Reads
Command line:
karma map -r reference.fa -c read1.fastq read2.fastq -o output.sam
