File Changes for vsmalladi

v259_preview to v259_preview2 (2011-10-25 to 2011-11-01) v259

• src/hg/encode/DAFs/3.0/hg19/wgEncodeBroadHistone.daf
  • lines changed 5, context: html, text, full: html, text
    Updated DAF to Version 1.8 to add treatment as a variable and removed peaks as required so that lab can submit controls.
  • lines changed 2, context: html, text, full: html, text
    Updated DAF to be correct composite which is Broad Histone.
• src/hg/encode/DAFs/3.0/hg19/wgEncodeUwRepliSeq.daf
  • lines changed 2, context: html, text, full: html, text
    Updated DAF say downloadOnly for Alignment files.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 24, context: html, text, full: html, text
    Meta-data for depercated file was left in by accident. Redmine 4558.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    Added metadata file for Uw Repli-seq track to makefile.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 5980, context: html, text, full: html, text
    Add 46 submission for track's second release. Redmine #4145.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 867, context: html, text, full: html, text
    Fixes Redmine #69 1. Fixed ordering of antibodies to be alphabetical AP-2α, AP-2γ then ATF3 2. Updated origAssembly. Inaddition added expVar for K562/JunD experiment that was missing it.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwRepliSeq.ra
  • lines changed 5587, context: html, text, full: html, text
    Added meta-data and initial display of peaks and Valley's as bed 9 files. Redmine 4577.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 3, context: html, text, full: html, text
    Preliminary comitting the Replication Seq Timing data. Redmine #4577.
  • lines changed 5, context: html, text, full: html, text
    Merge branch 'master' into UwReliSeq
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.new.ra
  • lines changed 1088, context: html, text, full: html, text
    Add 46 submission for track's second release. Redmine #4145.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 1, context: html, text, full: html, text
    Added back track line for track wgEncodeGisRnaPetNhekNucleusPapAlnRep.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra
  • lines changed 593, context: html, text, full: html, text
    Fixed errors found in Redmine #69 1. Updated the longLabels to be consnsitent with the terminology ChIP-seq instead of ChIP-Seq. 2. Removed nextItem button 3. Fixed so that all MCF10A-Er-Src stated control Standard as does its meta-data 4. Updated the track wgEncodeSydhTfbsGm12878Znf274StdSig to use the standard color for GM12878 cell line "153,38,0"
  • lines changed 1, context: html, text, full: html, text
    Fixes Redmine #69 1. Fixed ordering of antibodies to be alphabetical AP-2α, AP-2γ then ATF3 2. Updated origAssembly. Inaddition added expVar for K562/JunD experiment that was missing it.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 595, context: html, text, full: html, text
    Fixed errors found in Redmine #69 1. Updated the longLabels to be consnsitent with the terminology ChIP-seq instead of ChIP-Seq. 2. Removed nextItem button 3. Fixed so that all MCF10A-Er-Src stated control Standard as does its meta-data 4. Updated the track wgEncodeSydhTfbsGm12878Znf274StdSig to use the standard color for GM12878 cell line "153,38,0"
  • lines changed 1, context: html, text, full: html, text
    Fixes Redmine #69 1. Fixed ordering of antibodies to be alphabetical AP-2α, AP-2γ then ATF3 2. Updated origAssembly. Inaddition added expVar for K562/JunD experiment that was missing it.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
  • lines changed 4, context: html, text, full: html, text
    Updated tags for CD20 cell line to not include +, as configuration can only handle alphanumeric tags.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra
  • lines changed 1198, context: html, text, full: html, text
    Preliminary comitting the Replication Seq Timing data. Redmine #4577.
  • lines changed 219, context: html, text, full: html, text
    Added meta-data and initial display of peaks and Valley's as bed 9 files. Redmine 4577.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechHist.ra
  • lines changed 127, context: html, text, full: html, text
    Updated expId's and dccAccession for 2 tracks. Redmine #4155 and #4154.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechTfbs.ra
  • lines changed 247, context: html, text, full: html, text
    Updated expId's and dccAccession for 2 tracks. Redmine #4155 and #4154.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 2431, context: html, text, full: html, text
    Added 10 submission, three of which were previously submitted 3041,3042,3043. Redmine #111.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 817, context: html, text, full: html, text
    Added 3 submissions for track. Redmine #110.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.html
  • lines changed 6, context: html, text, full: html, text
    Fixes issues in Redmine #4155 1. Set diplay for Peaks to dense 2. Fixed the matrix hyperlinks for treatment and factor so they link to correct cv item. 3. Decreassed header size for "Rationale for the Mouse ENCODE project" 4. Updated the the following "An" -> "A" "consiting" -> "consisting" deleted duplicate the "contructed " -> "constructed" "avaialble " -> "available" "paramteres " -> "parameters"
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.ra
  • lines changed 4, context: html, text, full: html, text
    Fixes issues in Redmine #4155 1. Set diplay for Peaks to dense 2. Fixed the matrix hyperlinks for treatment and factor so they link to correct cv item. 3. Decreassed header size for "Rationale for the Mouse ENCODE project" 4. Updated the the following "An" -> "A" "consiting" -> "consisting" deleted duplicate the "contructed " -> "constructed" "avaialble " -> "available" "paramteres " -> "parameters"
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.html
  • lines changed 6, context: html, text, full: html, text
    Forgot thes files in commit:652519aed933b3d975c3feaa034873160f55cbf3 Fixes issues in Redmine #4154 1. Set diplay for Peaks to dense 2. Fixed the matrix hyperlinks for treatment and factor so they link to correct cv item. 3. Decreassed header size for "Rationale for the Mouse ENCODE project" 4. Updated the the following "An" -> "A" "consiting" -> "consisting" deleted duplicate the "contructed " -> "constructed" "avaialble " -> "available" "paramteres " -> "parameters"
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.new.ra
  • lines changed 4, context: html, text, full: html, text
    Forgot thes files in commit:652519aed933b3d975c3feaa034873160f55cbf3 Fixes issues in Redmine #4154 1. Set diplay for Peaks to dense 2. Fixed the matrix hyperlinks for treatment and factor so they link to correct cv item. 3. Decreassed header size for "Rationale for the Mouse ENCODE project" 4. Updated the the following "An" -> "A" "consiting" -> "consisting" deleted duplicate the "contructed " -> "constructed" "avaialble " -> "available" "paramteres " -> "parameters"
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.ra
  • lines changed 4, context: html, text, full: html, text
    Fixes issues in Redmine #4154 1. Set diplay for Peaks to dense 2. Fixed the matrix hyperlinks for treatment and factor so they link to correct cv item. 3. Decreassed header size for "Rationale for the Mouse ENCODE project" 4. Updated the the following "An" -> "A" "consiting" -> "consisting" deleted duplicate the "contructed " -> "constructed" "avaialble " -> "available" "paramteres " -> "parameters"
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
  • lines changed 243, context: html, text, full: html, text
    Added 10 submission, three of which were previously submitted 3041,3042,3043. Redmine #111.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
  • lines changed 55, context: html, text, full: html, text
    Added 3 submissions for track. Redmine #110.