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4
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1 This is a wrapper for a set of eQTL analysis tools.
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2
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3 Though, currently only PANAMA is supported.
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4 PANAMA takes in input as :
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5
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6 $panama expression_data.csv snp_data.csv
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7
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8 Where expression_data.csv is a Comma Separated Values file containing the gene expression data
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9 in the following format:
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10
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11 sample1, sample2, ..., sampleN
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12 gene1 value , value , ..., value
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13 gene2 value , value , ..., value
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14 ...
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15 geneN
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16
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17 and snp_data.csv contains the SNP data encoded as [0,1,2] in the following format:
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18
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19 sample1, sample2, ..., sampleN
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20 SNP1 value , value , ..., value
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21 SNP2 value , value , ..., value
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22 ...
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23 SNPQ
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24
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25 Make sure panama is installed and available on your path for all nodes.
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26 Move the test-data files to your galaxy root test-data folder and
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27 create a directory galaxy-central/tools/eqtl_tools and put
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28 the panama_run.py and panama.xml files inside eqtl_tools directory.
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