File Changes for vsmalladi

v253_preview to v253_preview2 (2011-06-14 to 2011-06-21) v253

• src/hg/encode/DAFs/2.0/caltechMm9Histone.daf
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    Updated DAF's to have replicates required for peaks and signals.
• src/hg/encode/DAFs/2.0/caltechMm9Tfbs.daf
  • lines changed 2, context: html, text, full: html, text
    Updated DAF's to have replicates required for peaks and signals.
• src/hg/encode/DAFs/2.0/uwMm9RnaSeq.daf
  • lines changed 60, context: html, text, full: html, text
    First pass at DAF for UW RNA-seq data.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
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    Updated the coloring shcema for mouse cell/tissues based on Redmine #3990. Also updated tissue of Muscle and Myocyte to be Muscles instead of blood. Limb and Placenta coloring needs to be worked on, will do more research, but added temporary coloring.
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    Changed coloring for Limb to Skeletal, makes the most sense at the moment. Also updated Placenta to be circulatory, as this is one of the main functions.
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    Fixed accidental mouse color reversions to match correct designation as Redmine 3990 and match commit 06dfd5c15b45b6253fa07b9599e799ca6b56ca56.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 47, context: html, text, full: html, text
    Removed duplcate objects on request from lab: wgEncodeHudsonalphaChipSeqRawSignalRep2Pfsk1Control and wgEncodeHudsonalphaChipSeqAlignmentsRep2Pfsk1Control.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
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    Removed duplcate objects on request from lab: wgEncodeHudsonalphaChipSeqRawSignalRep2Pfsk1Control and wgEncodeHudsonalphaChipSeqAlignmentsRep2Pfsk1Control.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 171, context: html, text, full: html, text
    Initial meta-data corrections to make sure experiments are correctly parsed for hg19.
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    Removed duplicate meta-data and raw-data files for K562 GTF2b experiment. Also correct type in load of GM12878 WHIP as GM112878 XRCC4. Delete older copy of GM12878 WHIP and Replaced with new file and update meta-data.
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    Removed old rawData file: wgEncodeSydhTfbsK562InputRawData that was moved from hg18 but has substitued data on hg19.
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    Updated lab meta-data so that experimetns would group together and would have same Ids as hg18.
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    Merged in changes that added 120 Peaks provided by awg.
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    Accidently committed meta-data file over trackDb file: 58d9a475183299f90ca6eb4ad34d31aa3cf01b52. Now did:Updated lab information for experiments such that they will group with the correct experiment number.
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    Added back metadata for submission 4119.
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    Added 3 missing Signals for track. Resolves redmine #3996.
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    Addedmissing bams for 2 experiemnts. Resolves issue in redmine #78. Also loaded bam's that were once concatenated submission 1625 and 1623 using samtools merge instead of cat. Resolves issue in redmine #3216.
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    Added last missing bam. Resolves Redmine #78
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 10, context: html, text, full: html, text
    Removed duplicate meta-data and raw-data files for K562 GTF2b experiment. Also correct type in load of GM12878 WHIP as GM112878 XRCC4. Delete older copy of GM12878 WHIP and Replaced with new file and update meta-data.
  • lines changed 287, context: html, text, full: html, text
    Merged in changes that added 120 Peaks provided by awg.
  • lines changed 38937, context: html, text, full: html, text
    Updated lab information for experiments such that they will group with the correct experiment number.
  • lines changed 38937, context: html, text, full: html, text
    Accidently committed meta-data file over trackDb file: 58d9a475183299f90ca6eb4ad34d31aa3cf01b52. Now did:Updated lab information for experiments such that they will group with the correct experiment number.
  • lines changed 25, context: html, text, full: html, text
    Added 3 missing Signals for track. Resolves redmine #3996.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 147, context: html, text, full: html, text
    Added submission 3057.
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    Updated meta-data and file and obj names with resbumitted bam's. Fixes Redmine Issue #2006.
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    Standardized the lab to be Stanford-m instead of just Stanford for mouse tracks.
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    Updated expVars for these tracks to include control, so that the correct inputs are experimentified.
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    Updated lab for bam files to match lab of other files for an experiment.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
  • lines changed 10, context: html, text, full: html, text
    Standardized the lab to be Stanford-m instead of just Stanford for mouse tracks.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 176, context: html, text, full: html, text
    Updated meta-data and file and obj names with resbumitted bam's. Fixes Redmine Issue #2006.
  • lines changed 26, context: html, text, full: html, text
    Removed meta-data for non-existant fastq and update file name for wgEncodeSydhTfbsMelInputStdAlnRep1 so that metaCheck would not complain.
  • lines changed 26, context: html, text, full: html, text
    Removed wgEncodeSydhTfbsMelInputIggyaleAlnRep1, as this experiment control is only used on The Histone Track.
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    Removed wgEncodeSydhTfbsCh12InputIggyaleAlnRep1, as this experiment control is only used on The Histone Track.
  • lines changed 59, context: html, text, full: html, text
    Standardized the lab to be Stanford-m instead of just Stanford for mouse tracks.
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    Added last fixed alignment wgEncodeSydhTfbsCh12InputIggrabAln, update object and file names.Fixes Redmine Issue #2006
  • lines changed 2, context: html, text, full: html, text
    Updated expVars for these tracks to include control, so that the correct inputs are experimentified.
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    Updated the correct meta-data for resubmitted Mel Max files. SubId 4157.
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    Revert "Updated the correct meta-data for resubmitted Mel Max files. SubId 4157." This reverts commit f3565a8b9028b97b8607b02f03173190255a5728.
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    Updated the correct meta-data for resubmitted Mel Max files (IgG-rab control instead of IgG-mus). SubId 4157.
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    Renamed 4 files for renaming DMSO Experiments that were missed earlier.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html
  • lines changed 2, context: html, text, full: html, text
    Removed references to pValue and qValue in tracks since Peaks don't have pValue or qValue. Resolves #957, note #15.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra
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    Fixed controlledVocabulary line in trackDb such that vocabulary in matix dimension link out to the correct terms in the cv.
  • lines changed 4, context: html, text, full: html, text
    Removed references to pValue and qValue in tracks since Peaks don't have pValue or qValue. Resolves #957, note #15.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed controlledVocabulary line in trackDb such that vocabulary in matix dimension link out to the correct terms in the cv.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html
  • lines changed 2, context: html, text, full: html, text
    Removed references to pValue and qValue in tracks since Peaks don't have pValue or qValue. Resolves #957, note #15.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed controlledVocabulary line in trackDb such that vocabulary in matix dimension link out to the correct terms in the cv.
  • lines changed 4, context: html, text, full: html, text
    Removed references to pValue and qValue in tracks since Peaks don't have pValue or qValue. Resolves #957, note #15.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra
  • lines changed 21, context: html, text, full: html, text
    Added submission 3057.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
  • lines changed 2, context: html, text, full: html, text
    Renamed 4 files for renaming DMSO Experiments that were missed earlier.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.html
  • lines changed 17, context: html, text, full: html, text
    Updated the ordering of the references to be alphabtically by first author. Added periods after article name to match standard. Redmine 191, note 17.