tdreszer: changes by file

branch to review (2009-09-29 to 2009-10-06) v217

• src/hg/encode/DAFs/UwDgf.daf
  • 1.1 lines changed: 56, context: html, text, full: html, text
    Initial version of UW Digital Genomic Footprinting DAF
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.195 lines changed: 4, context: html, text, full: html, text
    Support bed3s
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.133 lines changed: 1, context: html, text, full: html, text
    Sorry changing NFkB back to NFKB as this seems to be a valid term in the literature
  • 1.132 lines changed: 40, context: html, text, full: html, text
    For Yale added NF-YA and NF-YB and renamed NFKB to NFkB
  • 1.131 lines changed: 15, context: html, text, full: html, text
    Added antibody NFKB and treatment TNFa for Yale.
• src/hg/lib/wigAsciiToBinary.c
  • 1.33 lines changed: 19, context: html, text, full: html, text
    Reverting Hiram's changes temporarily, since ENCODE pipeline is now failing validation left and right
• src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt
  • 1.5 lines changed: 121, context: html, text, full: html, text
    Finished up the Sep 2009 freeze submissions with Melissa's help
• src/hg/makeDb/doc/encodeDccHg18/gencode.txt
  • 1.3 lines changed: 336, context: html, text, full: html, text
    Thought I should check in old stuff done for Gencode Release 3. Two issues still unresolved, though
• src/hg/makeDb/doc/encodeDccHg18/myers.txt
  • 1.3 lines changed: 46, context: html, text, full: html, text
    Tim adds some preliminary notes. No activity seen for Sept 2009 freeze
• src/hg/makeDb/doc/encodeDccHg18/nhgriNreBipElnitski.txt
  • 1.3 lines changed: 17, context: html, text, full: html, text
    Finally checking in some antient notes
• src/hg/makeDb/doc/encodeDccHg18/uwStam.txt
  • 1.1 lines changed: 253, context: html, text, full: html, text
    Added a lot of ChIPseq and DNase as part of the Sept 2009 freeze. Tracy Ballinger helped with trackDb, fileDb
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.561 lines changed: 35, context: html, text, full: html, text
    Finxed HeLa and HepG2 sort order in UW Dnase and ChIP
  • 1.560 lines changed: 1179, context: html, text, full: html, text
    Did some Broad track reordering
  • 1.559 lines changed: 31, context: html, text, full: html, text
    Left out UW ChIP HUVEC CTCF rep1 from last night's checkins
  • 1.558 lines changed: 146, context: html, text, full: html, text
    Its ChIP-seq not ChIP-Seq
  • 1.557 lines changed: 1027, context: html, text, full: html, text
    Reorganized UW DNase
  • 1.556 lines changed: 3, context: html, text, full: html, text
    Removed stray bad line. Changed UW DNase raw sig view range
  • 1.555 lines changed: 1514, context: html, text, full: html, text
    Added UW ChIPseq nad UW DNase. Reorganized a little