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 |