File Changes for vsmalladi

v252_preview2 to v252_base (2011-05-31 to 2011-06-07) v252

• src/hg/encode/DAFs/2.0/caltechMm9Histone.daf
  • lines changed 60, context: html, text, full: html, text
    Added first version of DAFs for Caltech MM9 submission for Histone, TFBS and RNA-seq tracks.
• src/hg/encode/DAFs/2.0/caltechMm9RnaSeq.daf
  • lines changed 87, context: html, text, full: html, text
    Added first version of DAFs for Caltech MM9 submission for Histone, TFBS and RNA-seq tracks.
• src/hg/encode/DAFs/2.0/caltechMm9Tfbs.daf
  • lines changed 60, context: html, text, full: html, text
    Added first version of DAFs for Caltech MM9 submission for Histone, TFBS and RNA-seq tracks.
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 3, context: html, text, full: html, text
    Added support for tgz to be tracked in notes files.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrHistone.release1.notes
  • lines changed 356, context: html, text, full: html, text
    Added release1 notes for the LICR Histone Track.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrRnaSeq.release1.notes
  • lines changed 224, context: html, text, full: html, text
    Added release1 notes for the LICR RNA-seq Track.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrTfbs.release1.notes
  • lines changed 383, context: html, text, full: html, text
    Added release1 notes for the LICR Tfbs Track.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeUwDnase.release1.notes
  • lines changed 596, context: html, text, full: html, text
    Added release1 notes for the UW DNaseI HS track.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 360, context: html, text, full: html, text
    Fixed errors found in code review when recovering 8 cell lines.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 397, context: html, text, full: html, text
    Added missing control files, as referenced in redmine 825.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Added new release in for updates to TFBS Haib track.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.new.ra
  • lines changed 1, context: html, text, full: html, text
    Changed windowing function from mean -> mean+whiskers as stated by QA in Redmine #1319.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 2649, context: html, text, full: html, text
    Added 120/122 missing Peaks from AWG. Redmine #3996.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 1057, context: html, text, full: html, text
    Added 120/122 missing Peaks from AWG. Redmine #3996.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimet defining variables.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed the naming of Signal table for Liver Replicate 2 to be wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep2 to match new file name. Also added commented out release tag for release 2 of UwDnase data that include Heart and TReg with only 1 replicate.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra
  • lines changed 97, context: html, text, full: html, text
    Updated coloring and short labels for track. (First pass)
  • lines changed 12, context: html, text, full: html, text
    Abbreviated Bone Marrow and Cerebellum for short labels.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.html
  • lines changed 2, context: html, text, full: html, text
    Removed first person narrative in track description. Added space to polA+RNA. Updated subGroup labels for longPolyA+ -> PolyA+, cell -> Whole Cell to match Human track labeling standards.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.ra
  • lines changed 103, context: html, text, full: html, text
    Updated notes and short and long labels for track. (First pass)
  • lines changed 36, context: html, text, full: html, text
    Updated coloring. Redmine 3990
  • lines changed 10, context: html, text, full: html, text
    Abbreviated Bone Marrow and Cerebellum for short labels.
  • lines changed 2, context: html, text, full: html, text
    Removed first person narrative in track description. Added space to polA+RNA. Updated subGroup labels for longPolyA+ -> PolyA+, cell -> Whole Cell to match Human track labeling standards.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra
  • lines changed 103, context: html, text, full: html, text
    Updated coloring and short labels for track.
  • lines changed 12, context: html, text, full: html, text
    Abbreviated Bone Marrow and Cerebellum for short labels.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.new.ra
  • lines changed 1725, context: html, text, full: html, text
    Removed replicate 1's of Heart and TReg experiments, as per advisment of Mouse ENCODE group. Only experiments with 2 replicates will be released. Made new.ra to house Heart and TReg replicate 1 for release 2.
  • lines changed 2, context: html, text, full: html, text
    Fixed the naming of Signal table for Liver Replicate 2 to be wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep2 to match new file name. Also added commented out release tag for release 2 of UwDnase data that include Heart and TReg with only 1 replicate.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra
  • lines changed 297, context: html, text, full: html, text
    Updated track settings. Update long and short labels to provide the most information. First pass at labels.
  • lines changed 81, context: html, text, full: html, text
    Updated color schema to organ systems.
  • lines changed 20, context: html, text, full: html, text
    Updated default tracks on to be replicate 1 and added cell line 3134. Also update windowing function from maximum -> mean+whiskers.
  • lines changed 7, context: html, text, full: html, text
    Abbreviated Bone Marrow and Cerebellum for short labels.
  • lines changed 56, context: html, text, full: html, text
    Removed replicate 1's of Heart and TReg experiments, as per advisment of Mouse ENCODE group. Only experiments with 2 replicates will be released. Made new.ra to house Heart and TReg replicate 1 for release 2.
  • lines changed 2, context: html, text, full: html, text
    Fixed the naming of Signal table for Liver Replicate 2 to be wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep2 to match new file name. Also added commented out release tag for release 2 of UwDnase data that include Heart and TReg with only 1 replicate.