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1 ======================================================================
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2 frequency_sliding
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3 ======================================================================
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4 ### This is the fourth tool in the eQTL backend pipeline:
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5 lookup, classification, frequency, sliding window frequency, hotspots, GO enrichment
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6
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7 Link to the workflow (for import into Galaxy): http://chewbacca.bi.up.ac.za:8080/u/nanette/w/back-end-workflow-2
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8
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9 Combine x cM intervals (size of lookup bins; for example 2 cM), to be used in a sliding window approach.
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10
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11 For 2 cM lookup bins:
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12
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13 * For two intervals per sliding window, intervals smaller than 2 cM are combined with its two flanking 2 cM intervals.
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14 Calculate the number of eQTLs per sliding window (4 - 5.9 cM intervals).
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15 Calculate the number of genes per sliding window (4 - 5.9 cM intervals).
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16
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17 * For three intervals per sliding window, intervals smaller than 2 cM are combined with 3 flanking 2 cM intervals.
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18 Calculate the number of eQTLs per sliding window (6 - 7.9 cM intervals).
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19 Calculate the number of genes per sliding window (6 - 7.9 cM intervals).
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20
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21
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22 ---------------
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23 Installation
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24 ---------------
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25
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26 The eQTL backend pipeline is available for:
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27 * command line usage
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28 * integration into Galaxy servers
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29
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30
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31 Requirements: Python 2.7
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32 R 3.1.1 |