File Changes for vsmalladi

v253_base to v254_preview (2011-06-28 to 2011-07-05) v254

• src/hg/encode/DAFs/2.0/uwMm9DnaseSeq.daf
  • lines changed 3, context: html, text, full: html, text
    Updated View Raw Signal -> Signal as request by lab.
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 2, context: html, text, full: html, text
    Removed accidentental changes by Morgan restored commit 4ee524db8c5e8f8d510ad5b53fd057b827ceaa3d. Also forced gbdb_path into string since it can return type None and can't be printed as type None.
  • lines changed 4, context: html, text, full: html, text
    Fixed logic error in Krish's script that placed unchanged bai and removed bai files in new files list.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhHistone.release1.notes
  • lines changed 97, context: html, text, full: html, text
    Added release 1 notes for track.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhTfbs.release2.notes
  • lines changed 568, context: html, text, full: html, text
    First pass at the making notes file for release 2 of file.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeUwDnase.release1.notes
  • lines changed 1, context: html, text, full: html, text
    Fixed Total field to have 114 tables that should be passed to RR. The 165 tables that were there indicate some tables that are for attic files.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 4, context: html, text, full: html, text
    Updated the Description for Yale-m to explictily state that Sherm Weissman did some of the experiments at Yale.
  • lines changed 19, context: html, text, full: html, text
    Added C2C12 cell line for Wold lab.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 48, context: html, text, full: html, text
    Removed experiment lab=HudsonAlpha dataType=ChipSeq cell=K562 antibody=Input treatment=None protocol=PCR2x, as this is not linked as a control for any experiment. Redmine #70, note 29 and Redmine #825, note 20.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
  • lines changed 8, context: html, text, full: html, text
    Removed experiment lab=HudsonAlpha dataType=ChipSeq cell=K562 antibody=Input treatment=None protocol=PCR2x, as this is not linked as a control for any experiment. Redmine #70, note 29 and Redmine #825, note 20.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 155, context: html, text, full: html, text
    Removed meta-data for version 1 of files and stored Geo Sample number ind dccInternalNotes for the V2 of the file for reference.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
  • lines changed 2, context: html, text, full: html, text
    Added first 23 submissions for track.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 2, context: html, text, full: html, text
    Fixed spelling of antibody in expVars.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 77, context: html, text, full: html, text
    Added missing control IgG-Yale DMSO control for Histone track that was on TFBS track (Redmine 97). Fixed last open concatenated bam bug wgEncodeSydhTfbsMelInputDmso20StdAln using submission 4327. (Redmine #3216)
  • lines changed 19, context: html, text, full: html, text
    Fixed lab's from Stanford-m to Yale-m as suggested by lab.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
  • lines changed 6, context: html, text, full: html, text
    Added expVars for track.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 4, context: html, text, full: html, text
    Added missing control IgG-Yale DMSO control for Histone track that was on TFBS track (Redmine 97). Fixed last open concatenated bam bug wgEncodeSydhTfbsMelInputDmso20StdAln using submission 4327. (Redmine #3216)
  • lines changed 147, context: html, text, full: html, text
    Forgot to add meta-data for submission 2540.
  • lines changed 191, context: html, text, full: html, text
    Updated lab from Stanford-m to Yale-m for 3 experiemnts (MEL DMSO CTCF, CH12 CTCF, MEL DMSO Input). Updated control from Std to IgG-rab for 3 experiements (MEL p300 Std, MEL SMC3 Std and MEL CTCF Std). Also updated the antibody for MEL CTCF Std to CTCF_(SC-15914). Redmine #2726, note 3.
  • lines changed 51, context: html, text, full: html, text
    Replaced subId 1859 with submission 4451.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 49, context: html, text, full: html, text
    Fixed one item that's meta-data didn't get renamed from Raw to Sig: wgEncodeUwDnaseLiverC57bl6MAdult8wksRawRep2. Fixes Redmine #191, Note:#31.
  • lines changed 1189, context: html, text, full: html, text
    Added 11 new submission for this track.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
  • lines changed 2743, context: html, text, full: html, text
    Added first 23 submissions for track.
  • lines changed 59, context: html, text, full: html, text
    Fixed metadata for submission 4443 and 4441.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Added first 23 submissions for track.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra
  • lines changed 8, context: html, text, full: html, text
    Updated colors of CH12 and MEL for the TFBS and Histone track. This conforms to the new colors in the cv.ra.
  • lines changed 38, context: html, text, full: html, text
    Updated notes for long and short labels. Update default tracks on and short and long labels for DMSO treated experiments.
  • lines changed 9, context: html, text, full: html, text
    Added missing control IgG-Yale DMSO control for Histone track that was on TFBS track (Redmine 97). Fixed last open concatenated bam bug wgEncodeSydhTfbsMelInputDmso20StdAln using submission 4327. (Redmine #3216)
  • lines changed 6, context: html, text, full: html, text
    Updated the DMSO tag's to match CV so that new items can easily be added into the track.
  • lines changed 2, context: html, text, full: html, text
    Updated track default settings and added fileSortOrder.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
  • lines changed 84, context: html, text, full: html, text
    Updated colors of CH12 and MEL for the TFBS and Histone track. This conforms to the new colors in the cv.ra.
  • lines changed 164, context: html, text, full: html, text
    Updated notes of long, short labels and abbreviations. Also, updated subGroups treatment to force None to sort last. First pass at long and short labels.
  • lines changed 9, context: html, text, full: html, text
    Updated the DMSO tag's to match CV so that new items can easily be added into the track.
  • lines changed 18, context: html, text, full: html, text
    Added submission 2540.
  • lines changed 17, context: html, text, full: html, text
    Updated default tracks on and off and accompanying notes. Aso updated p300sc584 -> p300sc584.
  • lines changed 22, context: html, text, full: html, text
    Updated lab from Stanford-m to Yale-m for 3 experiemnts (MEL DMSO CTCF, CH12 CTCF, MEL DMSO Input). Updated control from Std to IgG-rab for 3 experiements (MEL p300 Std, MEL SMC3 Std and MEL CTCF Std). Also updated the antibody for MEL CTCF Std to CTCF_(SC-15914). Redmine #2726, note 3.
  • lines changed 2, context: html, text, full: html, text
    Updated track default settings and added fileSortOrder.
  • lines changed 38, context: html, text, full: html, text
    Replaced subId 1859 with submission 4451.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.new.ra
  • lines changed 477, context: html, text, full: html, text
    Added 11 new submission for this track.
  • lines changed 5, context: html, text, full: html, text
    Added changes to Second release that were updated in Release 1 of track in Redmine #191. Also added Score Shading to both releases Redmine #191, note #33.
  • lines changed 1, context: html, text, full: html, text
    Added scoreMin for use to be able to change gray scale %. Redmine #191, note 36. Forgot in pervious commit.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra
  • lines changed 1, context: html, text, full: html, text
    Added changes to Second release that were updated in Release 1 of track in Redmine #191. Also added Score Shading to both releases Redmine #191, note #33.
  • lines changed 1, context: html, text, full: html, text
    Added scoreMin for use to be able to change gray scale %. Redmine #191, note 36. Forgot in pervious commit.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra
  • lines changed 937, context: html, text, full: html, text
    Added first 23 submissions for track.
  • lines changed 144, context: html, text, full: html, text
    Fixed metadata for submission 4443 and 4441.