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1 #This is a sample file distributed with Galaxy that enables the DC_Genotyper
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2 #tool to locate genome files for use with twoBitToFa, and IGVtools. You will
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3 #need to supply these files and then create a DC_Genotyper.loc file
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4 #similar to this one (store it in this directory) that points to
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5 #the directories in which those files are stored. The DC_Genotyper.loc
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6 #file has this format (white space characters are TAB characters):
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7 #
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8 #<unique_build_id> <dbkey> <display_name> <2bit_path,IGVtools_genome.path>
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9 #
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10 #for example:
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11 #
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12 #hg19 hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit,/depot/data2/galaxy/igvtools/hg19.chrom.sizes
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13 #
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14 #then your /depot/data2/galaxy/twobit/ directory
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15 #would need to contain the following 2bit files:
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16 #
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17 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit
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18 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit
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19 #
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20 # your igvtools folder needs the following files:
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21 #
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22 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.chrom.sizes
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23 #
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24 # igv chrom.sizes files are tab delimited files. First column is chromosome name, second column is length. Additional columns are ignored.
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25 # example genome files are included in the installation location of the package_igvtools repository.
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26
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