[2] | 1 | #This is a sample file distributed with Galaxy that is used by the |
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| 2 | #liftOver tools. The liftOver.loc file has this format (white space |
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| 3 | #characters are TAB characters): |
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| 4 | # |
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| 5 | #<FromSpecies> <ToSpecies> <PathToChainFile> |
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| 6 | # |
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| 7 | #So, for example, if you had the chain file to convert from anoCar1 to galGal3 |
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| 8 | #located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, |
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| 9 | #then the liftOver.loc entry would look like this: |
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| 10 | # |
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| 11 | #anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain |
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| 12 | # |
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| 13 | #and your /depot/data2/galaxy/anoCar1/liftOver directory would |
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| 14 | #contain all of your "chain" files (e.g.): |
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| 15 | # |
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| 16 | #-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain |
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| 17 | #-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain |
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| 18 | #-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain |
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| 19 | #...etc... |
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| 20 | # |
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| 21 | #Your liftOver.loc file should include an entry per line for each build you can |
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| 22 | #convert. For example: |
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| 23 | # |
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| 24 | #anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain |
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| 25 | #anoCar1 gasAcu1 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain |
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| 26 | #anoCar1 hg18 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain |
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| 27 | #...etc... |
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