--------------------------------------------------------------- nomLeu2.trackDb.html : Differences exist between hgwbeta and hgw2 (RR fields taken from public MySql server, not individual machine) 572,583d571 < cpgIslandExt |

< cpgIslandExt | The calculation of the track data is performed by the following command sequence: < cpgIslandExt |

< cpgIslandExt | twoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \\
< cpgIslandExt |   | cpg_lh /dev/stdin 2> cpg_lh.err \\
< cpgIslandExt |     |  awk '{$2 = $2 - 1; width = $3 - $2;  printf("%s\\t%d\\t%s\\t%s %s\\t%s\\t%s\\t%0.0f\\t%0.1f\\t%s\\t%s\
< cpgIslandExt | ", $1, $2, $3, $5, $6, width, $6, width*$7*0.01, 100.0*2*$6/width, $7, $9);}' \\
< cpgIslandExt |      | sort -k1,1 -k2,2n > cpgIsland.bed
< cpgIslandExt |

< cpgIslandExt | The unmasked track data is constructed from < cpgIslandExt | twoBitToFa -noMask output for the twoBitToFa command. < cpgIslandExt |

595,599d582 < cpgIslandExt |

< cpgIslandExt | The source for the cpg_lh program can be obtained from < cpgIslandExt | src/utils/cpgIslandExt/. < cpgIslandExt | The cpg_lh program binary can be obtained from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh (choose "save file") < cpgIslandExt |

677,688d659 < cpgIslandExtUnmasked |

< cpgIslandExtUnmasked | The calculation of the track data is performed by the following command sequence: < cpgIslandExtUnmasked |

< cpgIslandExtUnmasked | twoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \\
< cpgIslandExtUnmasked |   | cpg_lh /dev/stdin 2> cpg_lh.err \\
< cpgIslandExtUnmasked |     |  awk '{$2 = $2 - 1; width = $3 - $2;  printf("%s\\t%d\\t%s\\t%s %s\\t%s\\t%s\\t%0.0f\\t%0.1f\\t%s\\t%s\
< cpgIslandExtUnmasked | ", $1, $2, $3, $5, $6, width, $6, width*$7*0.01, 100.0*2*$6/width, $7, $9);}' \\
< cpgIslandExtUnmasked |      | sort -k1,1 -k2,2n > cpgIsland.bed
< cpgIslandExtUnmasked |

< cpgIslandExtUnmasked | The unmasked track data is constructed from < cpgIslandExtUnmasked | twoBitToFa -noMask output for the twoBitToFa command. < cpgIslandExtUnmasked |

700,704d670 < cpgIslandExtUnmasked |

< cpgIslandExtUnmasked | The source for the cpg_lh program can be obtained from < cpgIslandExtUnmasked | src/utils/cpgIslandExt/. < cpgIslandExtUnmasked | The cpg_lh program binary can be obtained from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh (choose "save file") < cpgIslandExtUnmasked |

782,793d747 < cpgIslandSuper |

< cpgIslandSuper | The calculation of the track data is performed by the following command sequence: < cpgIslandSuper |

< cpgIslandSuper | twoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \\
< cpgIslandSuper |   | cpg_lh /dev/stdin 2> cpg_lh.err \\
< cpgIslandSuper |     |  awk '{$2 = $2 - 1; width = $3 - $2;  printf("%s\\t%d\\t%s\\t%s %s\\t%s\\t%s\\t%0.0f\\t%0.1f\\t%s\\t%s\
< cpgIslandSuper | ", $1, $2, $3, $5, $6, width, $6, width*$7*0.01, 100.0*2*$6/width, $7, $9);}' \\
< cpgIslandSuper |      | sort -k1,1 -k2,2n > cpgIsland.bed
< cpgIslandSuper |

< cpgIslandSuper | The unmasked track data is constructed from < cpgIslandSuper | twoBitToFa -noMask output for the twoBitToFa command. < cpgIslandSuper |

805,809d758 < cpgIslandSuper |

< cpgIslandSuper | The source for the cpg_lh program can be obtained from < cpgIslandSuper | src/utils/cpgIslandExt/. < cpgIslandSuper | The cpg_lh program binary can be obtained from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh (choose "save file") < cpgIslandSuper |

1339,1343c1288 < rmsk | Repbase Update is described in Jurka (2000) in the References section below. < rmsk | Some newer assemblies have been made with Dfam, not Repbase. You can < rmsk | find the details for how we make our database data here in our "makeDb/doc/" < rmsk | directory.

--- > rmsk | Repbase Update is described in Jurka (2000) in the References section below.