Commits for vsmalladi

v246_base to v247_preview (2011-01-25 to 2011-02-01) v247

• Removed reference for submission 3249. Cell line used was incorrect and will reload data with newly registered HEK293 variant.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 131, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 18, context: html, text, full: html, text
• For submission 2093, the control used was incorrect. Changed IgG-Yale control to Standard Controls. This involved renaming files and tables and meta-data terms. THe ZZZ3 antibody was incorrect labeled in the trackDb as ZZZ3i, removed i to become ZZZ3.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 5, context: html, text, full: html, text
• Added comment line for Revision History.
  • src/hg/encode/DAFs/2.0/stanfordHg19Hist.daf - lines changed 1, context: html, text, full: html, text
• Changed the composite name from just Nsome to SydhNsome. This will had a lab tag so that the composite will be easily distinguished as other composites have this distintction.
  • src/hg/encode/DAFs/2.0/stanfordNucleosome.daf - lines changed 2, context: html, text, full: html, text
• Updated table, filename and track names for wgEncodeSydhTfbsHepg2Znf274Ucd experiments to be HepG2b instead of HepG2.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 9, context: html, text, full: html, text
• Updated table, filename and track names for wgEncodeSydhTfbsK562bKap1Ucd experiments to be K562b instead of K562.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 8, context: html, text, full: html, text
• MdbPrint to verify integrity of magic number.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 525, context: html, text, full: html, text
• Merge branch 'master' into Development
• Fixed error in DAF. Alignments expected tagAlign files however the type should be bam and match the validation settings.
  • src/hg/encode/DAFs/2.0/stanfordHg19Tfbs.daf - lines changed 1, context: html, text, full: html, text
• Displayed the first set of experiments from the University of Chicago.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra - lines changed 1219, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.ra - lines changed 185, context: html, text, full: html, text
• Added 14 submissions for the Jan 2011 Freeze.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 4013, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra - lines changed 880, context: html, text, full: html, text
• Added 16 submissions for Jan 2011 freeze.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 880, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra - lines changed 432, context: html, text, full: html, text
• Merge branch 'master' into Development
• Fixed naming of files, and tables for incorrectly tagged antibodyies for Mef2asc13268 -> Mef2csc13268 and Foxa1sc6554 -> Foxa2sc6554
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 41, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra - lines changed 8, context: html, text, full: html, text
• Merge branch 'master' into Development
• Added 9 submissions for the Jan 2011 freeze.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 1057, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 198, context: html, text, full: html, text
• Added replacement peaks (V2) for 5 cell lines. Removed the Version 1 references in trackDb.ra, but not in metaDb.ra.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra - lines changed 134, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra - lines changed 119, context: html, text, full: html, text
• Added replacement peaks (V2) for 8 cell lines-replicate pairs. Removed the Version 1 references in trackDb.ra, but not in metaDb.ra.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 161, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra - lines changed 146, context: html, text, full: html, text
• Fixed the standardization of dataType ChipSeq from ChIPseq -> ChipSeq.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 175, context: html, text, full: html, text
• Merge branch 'master' into Development
• Fixed the standardization of dataType ChipSeq from ChIPseq -> ChipSeq. Also replaced controlId None with correct controlId
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 34, context: html, text, full: html, text
• Changed lower case values of Sl -> SL to be consistent.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 20, context: html, text, full: html, text
• Add reference to metaData for Uchicago.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile - lines changed 2, context: html, text, full: html, text
• Removed all refrences to controlId None. Replaced using controlId provided by other fileTypes from the same experiment.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 6, context: html, text, full: html, text
• Fixed inconsistent labs from cv. Changed UCDavis -> UCD, UCD(Farnham) -> UCD and UNC(Lieb) -> UNC.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 61, context: html, text, full: html, text
• Merge branch 'master' into Development
• Merge branch 'master' into Development Conflicts: src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
• Patched up metaData file and objectnames with actual file names. Now all metaData maps 1:1 to a file.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 209, context: html, text, full: html, text
• Patched up metaData file with missing metaData and fixed mislabelled metaData.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 89, context: html, text, full: html, text
• Updated meta-data with correct controlId and labExpId using known experiments and excel sheet provided by preti found in redmine issue #420.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 200, context: html, text, full: html, text
• Fixed meta-data for experimetns with known controlId and expLabId's.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 8, context: html, text, full: html, text
• Removed all meta-data and tracks to reload data with better meta-data.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra - lines changed 1219, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.ra - lines changed 118, context: html, text, full: html, text
• Merge branch 'master' into Development
• Update meta-data and files with correct metaData.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra - lines changed 1219, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.ra - lines changed 120, context: html, text, full: html, text
• Merge branch 'Development'
• Added controlId and labExpId for raw data files that I was not able to correctly identify using experimental variables.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 27, context: html, text, full: html, text
• Merge branch 'Development'
• Corrected lab UCD(Farnham) -> UCD.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 7, context: html, text, full: html, text