--------------------------------------------------------------- panPan1.trackDb.html : Differences exist between hgwbeta and hgw2 (RR fields taken from public MySql server, not individual machine) 972,983d971 < 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 |

995,999d982 < 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 |

1077,1088d1059 < 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 |

1100,1104d1070 < 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 |

1182,1193d1147 < 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 |

1205,1209d1158 < 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 |

2245a2195,2213 > refSeqComposite |
  • > refSeqComposite | RefSeq Select+MANE (subset) – Subset of RefSeq Curated, transcripts marked as > refSeqComposite | RefSeq Select or MANE Select. > refSeqComposite | A single Select transcript is chosen as representative for each protein-coding gene. > refSeqComposite | This track includes transcripts categorized as MANE, which are further agreed upon as > refSeqComposite | representative by both NCBI RefSeq and Ensembl/GENCODE, and have a 100% identical match > refSeqComposite | to a transcript in the Ensembl annotation. See refSeqComposite | href="https://www.ncbi.nlm.nih.gov/refseq/refseq_select/">NCBI RefSeq Select. > refSeqComposite | Note that we provide a separate track, refSeqComposite | target=_blank href="hgTrackUi?g=mane&db=hg38&c=chr22">MANE (hg38), > refSeqComposite | which contains only the MANE transcripts. > refSeqComposite |
    • > refSeqComposite |
  • > refSeqComposite | RefSeq HGMD (subset) – Subset of RefSeq Curated, transcripts annotated by the Human > refSeqComposite | Gene Mutation Database. This track is only available on the human genomes hg19 and hg38. > refSeqComposite | It is the most restricted RefSeq subset, targeting clinical diagnostics. > refSeqComposite |
    • > refSeqComposite | > refSeqComposite | 2248,2249c2216,2217 < refSeqComposite | The RefSeq All, RefSeq Curated, RefSeq Predicted, and < refSeqComposite | UCSC RefSeq tracks follow the display conventions for --- > refSeqComposite | The RefSeq All, RefSeq Curated, RefSeq Predicted, RefSeq HGMD, > refSeqComposite | RefSeq Select/MANE and UCSC RefSeq tracks follow the display conventions for 2359,2360c2327 < refSeqComposite | using the REST API, < refSeqComposite | Table Browser or --- > refSeqComposite | using the Table Browser or 2381a2349,2350 > refSeqComposite |
  • RefSeq HGMD - ncbiRefSeqHgmd
    • > refSeqComposite |
  • RefSeq Select+MANE - ncbiRefSeqSelect
    • 2483,2487c2452 < 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.

    2610c2575 < ucscToINSDC | names from the ucscToINSDC | names from the