Mercurial > repos > nanettec > frequency_sliding
comparison 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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-1:000000000000 | 0:9b835eab8a1d |
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1 ====================================================================== | |
2 frequency_sliding | |
3 ====================================================================== | |
4 ### This is the fourth tool in the eQTL backend pipeline: | |
5 lookup, classification, frequency, sliding window frequency, hotspots, GO enrichment | |
6 | |
7 Link to the workflow (for import into Galaxy): http://chewbacca.bi.up.ac.za:8080/u/nanette/w/back-end-workflow-2 | |
8 | |
9 Combine x cM intervals (size of lookup bins; for example 2 cM), to be used in a sliding window approach. | |
10 | |
11 For 2 cM lookup bins: | |
12 | |
13 * For two intervals per sliding window, intervals smaller than 2 cM are combined with its two flanking 2 cM intervals. | |
14 Calculate the number of eQTLs per sliding window (4 - 5.9 cM intervals). | |
15 Calculate the number of genes per sliding window (4 - 5.9 cM intervals). | |
16 | |
17 * For three intervals per sliding window, intervals smaller than 2 cM are combined with 3 flanking 2 cM intervals. | |
18 Calculate the number of eQTLs per sliding window (6 - 7.9 cM intervals). | |
19 Calculate the number of genes per sliding window (6 - 7.9 cM intervals). | |
20 | |
21 | |
22 --------------- | |
23 Installation | |
24 --------------- | |
25 | |
26 The eQTL backend pipeline is available for: | |
27 * command line usage | |
28 * integration into Galaxy servers | |
29 | |
30 | |
31 Requirements: Python 2.7 | |
32 R 3.1.1 |