diff ETn_example/README.txt @ 12:af8c050ea4a9 draft

Uploaded 20170503
author fabio
date Wed, 03 May 2017 11:06:50 -0400
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+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.
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