Commits for vsmalladi

v246_preview2 to v246_base (2011-01-18 to 2011-01-25) v246

• Added 10 Chip-seq submissions for the Jan 2011 freeze.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 1706, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra - lines changed 367, context: html, text, full: html, text
• Added 29 submissions for the Jan 2011 Freeze. Also, removed commented lines out of trackDb and reorder treatment and antibodies in alphabetical order.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 3389, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 521, context: html, text, full: html, text
• Reordered tratments alphabetically.Missed in last commit.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 1, context: html, text, full: html, text
• Fixed controlId's for obj that had HeLaS3/None/Input/IgG-rab where cell line was miss spelled.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 7, context: html, text, full: html, text
• Fixed coding style to conform to camelCase of new subroutine. Also added whitespace after my decleration.
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 2, context: html, text, full: html, text
• Fixed miss spelling of Provisional
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 2, context: html, text, full: html, text
• Added new dataType Nucelosome.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 5, context: html, text, full: html, text
• Added 5 submissions for the Jan 2011 Freeze.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 641, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 101, context: html, text, full: html, text
• Added 4 submissions for the Jan 2011 Freeze.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 564, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra - lines changed 73, context: html, text, full: html, text
• Added 5 submissions with Peaks and Signals which previously only had raw data files.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 403, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra - lines changed 151, context: html, text, full: html, text
• Added LICR Histone track.
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 3, context: html, text, full: html, text
• Added 7 submissions of Peaks and Signals which previously only had raw data files.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 537, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra - lines changed 173, context: html, text, full: html, text
• Changed Long and Short labels to comply with track configuration standards.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra - lines changed 2, context: html, text, full: html, text
• Changed Long and Short labels to comply with track configuration standards.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra - lines changed 2, context: html, text, full: html, text
• Added new antibody for White lab: eGFP-NR4A1
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 15, context: html, text, full: html, text
• Added noInherit on to both tracks.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.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
• Fixed DAF so that Peaks and Signal will not be required for all experiments. Inputs generate ALignments and Raw Data only and are subtracted from experiments with antibodies to generate Peaks and Signals.
  • src/hg/encode/DAFs/2.0/uChicagoTfbs.daf - lines changed 3, context: html, text, full: html, text
• Added 8 antibodies for Myers lab that did not have validation documents.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 119, context: html, text, full: html, text
• Added new Seq Platform AB SOLiD 3 Plus
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 6, context: html, text, full: html, text
• Updated BAM validation to look for 99.9% of file that agrese with 3 mismatches.
  • src/hg/encode/DAFs/2.0/stanfordNucleosome.daf - lines changed 2, context: html, text, full: html, text
• Added new Control Terms for controls used when comparing for a specific antibody replicate. Lab doesn't use 1 run of a control to compare all results, but rather a control is run at the same time for each antibody specific experiment.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 30, context: html, text, full: html, text
• Removed errant space in shortlabl for 1 subtrack. ast by ChIP-seq to subtrack long labels to following track settings style guide.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra - lines changed 424, context: html, text, full: html, text