Mercurial > repos > fabio > iwtomics
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ETn_example/README.txt Wed May 03 11:06:50 2017 -0400 @@ -0,0 +1,21 @@ +This example contains two region datasets "ETn fixed", "Control" and one feature "Recombination hotspots content". +In particular, the region dataset "ETn fixed" contains 1296 genomic regions of 64 kb surrounding +fixed ETns elements (32-kb flanking sequences upstream and 32-kb flanking sequences downstream +of each element). The region dataset "Control" contains 1142 regions of 64 kb without elements, +used as control in the test. The regions are aligned around their center (i.e. around the ETn integration +sites). +Recombination hotspots measurements are associated to each "ETn fixed" and "Control" region. In +particular, this feature is measured in 1-kb windows, so that each region is associated to a recombination +hotspots curve made of 64 values. The measurement used is the feature content, i.e. the +fraction of the 1-kb window that is covered by recombination hotspots + +Data have been collected and pre-processed by: R Campos-Sanchez, MA Cremona, A Pini, F +Chiaromonte and KD Makova (2016). Integration and fixation preferences of human and mouse +endogenous retroviruses uncovered with Functional Data Analysis. PLoS Computational Biology. +12(6): 1-41. +Fixed ETn positions come from: Y Zhang, IA Maksakova, L Gagnier, LN van de Lagemaat, DL +Mager (2008). Genome-wide assessments reveal extremely high levels of polymorphism of two +active families of mouse endogenous retroviral elements. PLoS Genetics. 4: e1000007. +Recombination hotspots data come from: H Brunschwig, L Levi, E Ben-David, RW Williams, +B Yakir, S Shifman (2012). Fine-scale maps of recombination rates and hotspots in the mouse +genome. Genetics. 191: 757-764. \ No newline at end of file