Difference between revisions of "Karma"
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Jump to navigationJump to search (→Align Illumina Reads: fix argument order) |
(→Align ABI SOLiD Reads: fix argument order) |
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− | karma map -r reference.fa -c read1.fastq read2.fastq | + | karma map -r reference.fa -c -o output.sam read1.fastq read2.fastq |
</pre> | </pre> | ||
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= Other useful links = | = Other useful links = |
Revision as of 16:54, 7 April 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 -o output.sam read1.fastq read2.fastq
Align ABI SOLiD Reads
Command line:
karma map -r reference.fa -c -o output.sam read1.fastq read2.fastq