File Changes for vsmalladi

v247_preview to v247_preview2 (2011-02-01 to 2011-02-08) v247

• src/hg/encode/encodeValidate/config/expVars.ra
  • lines changed 57, context: html, text, full: html, text
    Added preliminary experimant defining vars for 12 tracks.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 211, context: html, text, full: html, text
    Added 13 bam files that were either missing or fixed tha had already been passed on to the AWG.
  • lines changed 7, context: html, text, full: html, text
    Update the conrolId for experiments where the initial control was bad. Changed SL1780 -> SL2455 for 3 replicates.
  • lines changed 42, context: html, text, full: html, text
    Fixed 11 experiments to have correct protocol's.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 11, context: html, text, full: html, text
    Fixed cell and controlId's for experiments where UCD was lab and lab has variant B of cell, but was incorrectly labeled with non-variant cell line.
  • lines changed 11, context: html, text, full: html, text
    Reversed the corrections in commit 9f9ec89fe3b8914f8cbc37e568293082a42e087e. Waiting on labs updates.
  • lines changed 25, context: html, text, full: html, text
    Updated meta-data errors when Anshul was mapping controls.
  • lines changed 31, context: html, text, full: html, text
    Fixed wrong antibody designations in meta-data. Changed HA-F2F1 -> HA-E2F1 and MafK_(sc477) -> MafK_(SC-477)
  • lines changed 3, context: html, text, full: html, text
    Fixed wrong antibody designations in meta-data that I forgot in last commit Changed HA-F2F1 -> HA-E2F1.
  • lines changed 3, context: html, text, full: html, text
    Replaced empty BAM file with submission 3500.
  • lines changed 63, context: html, text, full: html, text
    Added submission 3499, for missing T-REx HEK293 control input.
  • lines changed 187, context: html, text, full: html, text
    Addd submissions 3501,3497,3498. That fill gaps of missing controls for AWG.
  • lines changed 49, context: html, text, full: html, text
    Fixed incorrect controls and controlId's for MCF10A-Er-Src experiments.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 3, context: html, text, full: html, text
    Fixed cell and controlId's for experiments where UCD was lab and lab has variant B of cell, but was incorrectly labeled with non-variant cell line.
  • lines changed 3, context: html, text, full: html, text
    Reversed the corrections in commit 9f9ec89fe3b8914f8cbc37e568293082a42e087e. Waiting on labs updates.
  • lines changed 9, context: html, text, full: html, text
    Updated meta-data errors when Anshul was mapping controls.
  • lines changed 9, context: html, text, full: html, text
    Added submission 3499, for missing T-REx HEK293 control input.
  • lines changed 28, context: html, text, full: html, text
    Addd submissions 3501,3497,3498. That fill gaps of missing controls for AWG.
  • lines changed 8, context: html, text, full: html, text
    Fixed incorrect controls and controlId's for MCF10A-Er-Src experiments.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
  • lines changed 96, context: html, text, full: html, text
    Forced Tier 1 and Tier 2 cell lines to appear 1st and 2nd in the browswer before all tier 3 cell lines which are listed alphabetically.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.ra
  • lines changed 36, context: html, text, full: html, text
    Forced Tier 1 and Tier 2 cell lines to appear 1st and 2nd in the browswer before all tier 3 cell lines which are listed alphabetically.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 5, context: html, text, full: html, text
    Replaced two Peak files with newer versions. wgEncodeSydhTfbsMelCtcfDmso20IggyalePk and wgEncodeSydhTfbsMelRad21Dmso20IggrabPk.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.html
  • lines changed 2, context: html, text, full: html, text
    Added View for Alignments to state that it is available for download.
  • lines changed 9, context: html, text, full: html, text
    Added explanation of pooled data and link to per-replicate alignments and sequences. Also added explanation for Peaks grayscale.
  • lines changed 2, context: html, text, full: html, text
    Removed alignments from Display conventions.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
  • lines changed 57, context: html, text, full: html, text
    Fixed track longLabls to substitute Transcription Factor Binding -> TFBS by Chip-Seq
  • lines changed 2, context: html, text, full: html, text
    Replaced two Peak files with newer versions. wgEncodeSydhTfbsMelCtcfDmso20IggyalePk and wgEncodeSydhTfbsMelRad21Dmso20IggrabPk.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.ra
  • lines changed 2, context: html, text, full: html, text
    Replaced two Peak files with newer versions. wgEncodeSydhTfbsMelCtcfDmso20IggyalePk and wgEncodeSydhTfbsMelRad21Dmso20IggrabPk.
  • lines changed 1, context: html, text, full: html, text
    Commented out filterComposite option and replaced with checkboxes so that track can go out.