Commits for vsmalladi

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

• Initial meta-data corrections to make sure experiments are correctly parsed for hg19.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 171, 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.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 69, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 10, context: html, text, full: html, text
• Removed old rawData file: wgEncodeSydhTfbsK562InputRawData that was moved from hg18 but has substitued data on hg19.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 22, context: html, text, full: html, text
• Updated lab meta-data so that experimetns would group together and would have same Ids as hg18.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 1641, context: html, text, full: html, text
• Merged in changes that added 120 Peaks provided by awg.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 97, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 287, context: html, text, full: html, text
• Updated lab information for experiments such that they will group with the correct experiment number.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - 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.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 545, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 38937, context: html, text, full: html, text
• Merge branch 'master' into Sydh-Metadata
• Added back metadata for submission 4119.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 63, context: html, text, full: html, text
• Added submission 3057.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 147, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra - lines changed 21, context: html, text, full: html, text
• Merge branch 'master' into Sydh-Metadata
• Updated DAF's to have replicates required for peaks and signals.
  • src/hg/encode/DAFs/2.0/caltechMm9Histone.daf - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/caltechMm9Tfbs.daf - lines changed 2, context: html, text, full: html, text
• Merge branch 'master' into Development-Mouse
• Updated meta-data and file and obj names with resbumitted bam's. Fixes Redmine Issue #2006.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 41, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 176, 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.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 26, context: html, text, full: html, text
• Removed wgEncodeSydhTfbsMelInputIggyaleAlnRep1, as this experiment control is only used on The Histone Track.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 26, context: html, text, full: html, text
• Removed wgEncodeSydhTfbsCh12InputIggyaleAlnRep1, as this experiment control is only used on The Histone Track.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 25, 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/wgEncodeSydhHistone.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 59, context: html, text, full: html, text
• Added 3 missing Signals for track. Resolves redmine #3996.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 25, context: html, text, full: html, text
• Added last fixed alignment wgEncodeSydhTfbsCh12InputIggrabAln, update object and file names.Fixes Redmine Issue #2006
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 7, context: html, text, full: html, text
• Updated expVars for these tracks to include control, so that the correct inputs are experimentified.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 2, context: html, text, full: html, text
• Updated the correct meta-data for resubmitted Mel Max files. SubId 4157.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 5, context: html, text, full: html, text
• Revert "Updated the correct meta-data for resubmitted Mel Max files. SubId 4157." This reverts commit f3565a8b9028b97b8607b02f03173190255a5728.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 5, context: html, text, full: html, text
• Updated the correct meta-data for resubmitted Mel Max files (IgG-rab control instead of IgG-mus). SubId 4157.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 9, context: html, text, full: html, text
• Updated lab for bam files to match lab of other files for an experiment.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 4, context: html, text, full: html, text
• Renamed 4 files for renaming DMSO Experiments that were missed earlier.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra - lines changed 2, context: html, text, full: html, text
• Merge branch 'Development-Mouse'
• 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.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 72, context: html, text, full: html, text
• 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.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 39, context: html, text, full: html, text
• 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.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 2, 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/wgEncodeLicrHistone.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra - lines changed 1, 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.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra - lines changed 4, context: html, text, full: html, text
• First pass at DAF for UW RNA-seq data.
  • src/hg/encode/DAFs/2.0/uwMm9RnaSeq.daf - lines changed 60, context: html, text, full: html, text
• Removed duplcate objects on request from lab: wgEncodeHudsonalphaChipSeqRawSignalRep2Pfsk1Control and wgEncodeHudsonalphaChipSeqAlignmentsRep2Pfsk1Control.
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra - lines changed 47, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra - lines changed 7, context: html, text, full: html, text
• Added last missing bam. Resolves Redmine #78
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 24, context: html, text, full: html, text
• Merge branch 'master' into Sydh-Metadata Conflicts: src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
• Fixed accidental mouse color reversions to match correct designation as Redmine 3990 and match commit 06dfd5c15b45b6253fa07b9599e799ca6b56ca56.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 5, 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.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.html - lines changed 17, context: html, text, full: html, text