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, 09:07, 24 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] |
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− | * 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] |
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| 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] |
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| Defaults: | | Defaults: |
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| </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 |
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− | * File strucutre
| + | NCBI37.umwiwp |
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− | Color space mapping needs 6 files, and base space mapping needs 5 files (only need to use 1 reference genome).
| + | | |
| + | |- |
| + | | Word Hash (Left) |
| + | | NCBI37-bs15.umwhl |
| + | | |
| + | |- |
| + | | Word Hash (Right) |
| + | | NCBI37-bs15.umwhr |
| + | | |
| + | |} |
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− | Ue color space as an example, and say we use NCBI36.fa as reference genome:
| + | <br> |
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− | basespace.umfa => NCBI36.bs.umfa | + | basespace.umfa => NCBI36.bs.umfa |
− | colorspace.umfa => NCBI36.cs.umfa | + | colorspace.umfa => NCBI36.cs.umfa |
− | colorspace.umwhr => NCBI36.cs.12.umwhr | + | colorspace.umwhr => NCBI36.cs.12.umwhr |
− | colorspace.umwhl => NCBI36.cs.12.umwhl | + | colorspace.umwhl => NCBI36.cs.12.umwhl |
− | colorspace.umwihi => NCBI36.cs.12.umwihi | + | colorspace.umwihi => NCBI36.cs.12.umwihi |
− | colorspace.umwiwp => NCBI36.cs.12.umwiwp | + | colorspace.umwiwp => NCBI36.cs.12.umwiwp |
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− | * Other useful links: | + | *Other useful links: |
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− | [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] |
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− | [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] |
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| [http://lh3lh3.users.sourceforge.net/udb.shtml Benchmark of Dictionary Structures] | | [http://lh3lh3.users.sourceforge.net/udb.shtml Benchmark of Dictionary Structures] |