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, 17:36, 30 March 2010
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| Karma is top secret. Shh! | | Karma is top secret. Shh! |
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− | *Download
| + | = Download = |
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| 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
| + | = Build Reference = |
− | <pre>Usage:
| + | |
| + | == Options == |
| + | |
| + | Command line |
| + | |
| + | 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] |
− | Diagnostics: | + | |
| + | Diagnostics: |
| + | |
| karma88 check [options...] | | karma88 check [options...] |
− | karma88 test [options...]
| + | karma88 test [options...] |
− | -d -> debug
| + | -d -> debug |
− | -s [int] -> set random number seed [12345]
| + | -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) | |
| | | |
− | </pre>
| + | == File structure == |
− | *File strucutre
| |
| | | |
− | Color space mapping needs 6 files, and base space mapping needs 5 files (only need to use 1 reference genome).
| + | Upon successfully building references, you will obtain a list of reference files like below: |
− | | |
− | Ue color space as an example, and say we use NCBI36.fa as reference genome:
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| {| 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" |
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− | 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 |
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− | | NCBI37-cs.15.5000.umwiwp NCBI37-cs.15.5000.umwihi<br>
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| |- | | |- |
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| <br> | | <br> |
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− | basespace.umfa => NCBI36.bs.umfa
| + | <br> |
− | colorspace.umfa => NCBI36.cs.umfa
| + | |
− | colorspace.umwhr => NCBI36.cs.12.umwhr
| + | = Align Illumina Reads = |
− | colorspace.umwhl => NCBI36.cs.12.umwhl
| + | |
− | colorspace.umwihi => NCBI36.cs.12.umwihi
| + | Command line: |
− | colorspace.umwiwp => NCBI36.cs.12.umwiwp
| + | |
| + | <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:
| + | = 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] |