File Changes for vsmalladi

v248_preview2 to v248_base (2011-03-01 to 2011-03-08) v248

• src/hg/makeDb/doc/encodeDccMm9/wgEncodePsuHistone.release1.notes
  • lines changed 92, context: html, text, full: html, text
    Added release notes for PSU mm9 tracks.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodePsuTfbs.release1.notes
  • lines changed 121, context: html, text, full: html, text
    Added release notes for PSU mm9 tracks.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 17, context: html, text, full: html, text
    Removed duplication of MAX and MAX_(C-17). Sunseted MAX_(C-17) as no lab has used this distinction.
  • lines changed 10, context: html, text, full: html, text
    Added 5 cell growth protocols provided by UW (Stam lab).
  • lines changed 2, context: html, text, full: html, text
    G1E-E4+E2 Should be G1E-ER4+E2 . Fixed redmine issue 3508.
  • lines changed 1, context: html, text, full: html, text
    Fixed missing commit for 27f5162ffb937de52f5b234a24d9b6cc4e42cc2b. Updated unit spacing to be consistent with rest of browswer. Issue 59, note 30.
  • lines changed 1, context: html, text, full: html, text
    Updated description of the H3K79me2 description.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 3395, context: html, text, full: html, text
    First pass removal of 143 files (9 files are suspect due to meta-data inconsistenties, waiting on lab for proper procedure)
  • lines changed 49, context: html, text, full: html, text
    Removed reference to 7 files in metaDb and trackDb. Restored 2 files fully in browser.
  • lines changed 3259, context: html, text, full: html, text
    Moved 137 files that had meta-data problems that will be replaced.
  • lines changed 23, context: html, text, full: html, text
    Added meta-data for missing fastq in submission 3108.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 353, context: html, text, full: html, text
    Changed H3K4me3 -> H3K4me3B antibody variant.
  • lines changed 353, context: html, text, full: html, text
    Fixed object and table names that had H3K4me3b instead of H3k4me3b.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 22, context: html, text, full: html, text
    Removed extra meta-data for obj wgEncodeSydhTfbsHuvecInputUcdAln in metaDb.ra file.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 551, context: html, text, full: html, text
    First pass removal of 143 files (9 files are suspect due to meta-data inconsistenties, waiting on lab for proper procedure)
  • lines changed 40, context: html, text, full: html, text
    Removed reference to 7 files in metaDb and trackDb. Restored 2 files fully in browser.
  • lines changed 657, context: html, text, full: html, text
    Moved 137 files that had meta-data problems that will be replaced.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.ra
  • lines changed 19, context: html, text, full: html, text
    Changed H3K4me3 -> H3K4me3B antibody variant.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.ra
  • lines changed 258, context: html, text, full: html, text
    Updated composite long and short labels to new labels decided by Kate. Also updated view long labels: TFBS -> TFBS ChIP-seq. Redmine: 1604, note 22.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 211, context: html, text, full: html, text
    G1E-E4+E2 Should be G1E-ER4+E2 . Fixed redmine issue 3508.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 47, context: html, text, full: html, text
    G1E-E4+E2 Should be G1E-ER4+E2 . Fixed redmine issue 3508.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html
  • lines changed 180, context: html, text, full: html, text
    Added track description for LICR TFBS and Histone Modificiation tracks.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html
  • lines changed 180, context: html, text, full: html, text
    Added track description for LICR TFBS and Histone Modificiation tracks.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed error with broken controlled vocabulary links on track configuration page.
  • lines changed 25, context: html, text, full: html, text
    G1E-E4+E2 Should be G1E-ER4+E2 . Fixed redmine issue 3508.
  • lines changed 1, context: html, text, full: html, text
    Added fileSortOrder information for updated downloads page.
  • lines changed 25, context: html, text, full: html, text
    Added notes for track configuration. Also updated windowingFunction to maximum according to lab.
  • lines changed 15, context: html, text, full: html, text
    Updated short and long labels to follow ENCODE labeling standards.
  • lines changed 8, context: html, text, full: html, text
    First pass at short label shortening. Will ask Kate for opnions.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
  • lines changed 3, context: html, text, full: html, text
    Set Defaults to display all Cell-Antibody combinations, as there is very little data.
  • lines changed 1, context: html, text, full: html, text
    Fixed error with broken controlled vocabulary links on track configuration page.
  • lines changed 17, context: html, text, full: html, text
    G1E-E4+E2 Should be G1E-ER4+E2 . Fixed redmine issue 3508.
  • lines changed 1, context: html, text, full: html, text
    Added fileSortOrder information for updated downloads page.
  • lines changed 31, context: html, text, full: html, text
    Updated track comments with configuration. Removed Pol2-4H8 as a deafult track. Deafulted windowing function to maximum for Signal.
  • lines changed 1, context: html, text, full: html, text
    Updated note for track name.
  • lines changed 21, context: html, text, full: html, text
    Updated short and long labels to follow ENCODE labelling standards.
  • lines changed 11, context: html, text, full: html, text
    First pass at short label shortening. Will ask Kate for opnions.