Commits for vsmalladi

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

• Updated track settings. Update long and short labels to provide the most information. First pass at labels.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra - lines changed 297, context: html, text, full: html, text
• Updated color schema to organ systems.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra - lines changed 81, context: html, text, full: html, text
• Merge branch 'master' into Development-Mouse
• Changed windowing function from mean -> mean+whiskers as stated by QA in Redmine #1319.
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.new.ra - lines changed 1, context: html, text, full: html, text
• Merge branch 'master' into Development-Mouse
• Updated default tracks on to be replicate 1 and added cell line 3134. Also update windowing function from maximum -> mean+whiskers.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra - lines changed 20, context: html, text, full: html, text
• Updated coloring and short labels for track.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra - lines changed 103, context: html, text, full: html, text
• Updated coloring and short labels for track. (First pass)
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra - lines changed 97, context: html, text, full: html, text
• Fixed errors found in code review when recovering 8 cell lines.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 360, context: html, text, full: html, text
• Updated notes and short and long labels for track. (First pass)
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.ra - lines changed 103, context: html, text, full: html, text
• Updated coloring. Redmine 3990
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.ra - lines changed 36, context: html, text, full: html, text
• Abbreviated Bone Marrow and Cerebellum for short labels.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra - lines changed 7, 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.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.new.ra - lines changed 1725, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra - lines changed 56, 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/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.new.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra - lines changed 2, context: html, text, full: html, text
• Merge branch 'master' into Development-Mouse
• Added release1 notes for the LICR Histone Track.
  • src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrHistone.release1.notes - lines changed 356, context: html, text, full: html, text
• Added release1 notes for the LICR Tfbs Track.
  • src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrTfbs.release1.notes - lines changed 383, context: html, text, full: html, text
• Added release1 notes for the LICR RNA-seq Track.
  • src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrRnaSeq.release1.notes - lines changed 224, context: html, text, full: html, text
• Added support for tgz to be tracked in notes files.
  • src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes - lines changed 3, context: html, text, full: html, text
• Added release1 notes for the UW DNaseI HS track.
  • src/hg/makeDb/doc/encodeDccMm9/wgEncodeUwDnase.release1.notes - lines changed 596, context: html, text, full: html, text
• Added experimet defining variables.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra - lines changed 6, 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/caltechMm9Histone.daf - lines changed 60, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/caltechMm9RnaSeq.daf - lines changed 87, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/caltechMm9Tfbs.daf - lines changed 60, context: html, text, full: html, text
• Added missing control files, as referenced in redmine 825.
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra - lines changed 397, 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.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.ra - lines changed 2, context: html, text, full: html, text
• Added 120/122 missing Peaks from AWG. Redmine #3996.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 2649, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 1057, context: html, text, full: html, text
• Added new release in for updates to TFBS Haib track.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text