Mercurial > repos > fabio > iwtomics
comparison ETn_example/README.txt @ 12:af8c050ea4a9 draft
Uploaded 20170503
| author | fabio |
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| date | Wed, 03 May 2017 11:06:50 -0400 |
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comparison
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| 11:3a56f8e72534 | 12:af8c050ea4a9 |
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| 1 This example contains two region datasets "ETn fixed", "Control" and one feature "Recombination hotspots content". | |
| 2 In particular, the region dataset "ETn fixed" contains 1296 genomic regions of 64 kb surrounding | |
| 3 fixed ETns elements (32-kb flanking sequences upstream and 32-kb flanking sequences downstream | |
| 4 of each element). The region dataset "Control" contains 1142 regions of 64 kb without elements, | |
| 5 used as control in the test. The regions are aligned around their center (i.e. around the ETn integration | |
| 6 sites). | |
| 7 Recombination hotspots measurements are associated to each "ETn fixed" and "Control" region. In | |
| 8 particular, this feature is measured in 1-kb windows, so that each region is associated to a recombination | |
| 9 hotspots curve made of 64 values. The measurement used is the feature content, i.e. the | |
| 10 fraction of the 1-kb window that is covered by recombination hotspots | |
| 11 | |
| 12 Data have been collected and pre-processed by: R Campos-Sanchez, MA Cremona, A Pini, F | |
| 13 Chiaromonte and KD Makova (2016). Integration and fixation preferences of human and mouse | |
| 14 endogenous retroviruses uncovered with Functional Data Analysis. PLoS Computational Biology. | |
| 15 12(6): 1-41. | |
| 16 Fixed ETn positions come from: Y Zhang, IA Maksakova, L Gagnier, LN van de Lagemaat, DL | |
| 17 Mager (2008). Genome-wide assessments reveal extremely high levels of polymorphism of two | |
| 18 active families of mouse endogenous retroviral elements. PLoS Genetics. 4: e1000007. | |
| 19 Recombination hotspots data come from: H Brunschwig, L Levi, E Ben-David, RW Williams, | |
| 20 B Yakir, S Shifman (2012). Fine-scale maps of recombination rates and hotspots in the mouse | |
| 21 genome. Genetics. 191: 757-764. |