Mercurial > repos > nanettec > frequency_sliding
diff frequency_sliding/readme.txt @ 0:9b835eab8a1d draft
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author | nanettec |
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date | Fri, 18 Mar 2016 05:22:30 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/frequency_sliding/readme.txt Fri Mar 18 05:22:30 2016 -0400 @@ -0,0 +1,32 @@ +====================================================================== +frequency_sliding +====================================================================== +### This is the fourth tool in the eQTL backend pipeline: +lookup, classification, frequency, sliding window frequency, hotspots, GO enrichment + +Link to the workflow (for import into Galaxy): http://chewbacca.bi.up.ac.za:8080/u/nanette/w/back-end-workflow-2 + +Combine x cM intervals (size of lookup bins; for example 2 cM), to be used in a sliding window approach. + +For 2 cM lookup bins: + +* For two intervals per sliding window, intervals smaller than 2 cM are combined with its two flanking 2 cM intervals. +Calculate the number of eQTLs per sliding window (4 - 5.9 cM intervals). +Calculate the number of genes per sliding window (4 - 5.9 cM intervals). + +* For three intervals per sliding window, intervals smaller than 2 cM are combined with 3 flanking 2 cM intervals. +Calculate the number of eQTLs per sliding window (6 - 7.9 cM intervals). +Calculate the number of genes per sliding window (6 - 7.9 cM intervals). + + +--------------- +Installation +--------------- + +The eQTL backend pipeline is available for: +* command line usage +* integration into Galaxy servers + + +Requirements: Python 2.7 + R 3.1.1 \ No newline at end of file