File Changes for vsmalladi

v263_preview2 to v263_base (2011-02-07 to 2012-02-14) v263

• src/hg/encode/DAFs/3.0/hg19/wgEncodeFsuRepliSeq.daf
  • lines changed 41, context: html, text, full: html, text
    Added cv items for new repli-seq data from Gilbert lab. Also took the first stab at a DAF for the Human data set. Redmine #6627, #6626.
  • lines changed 1, context: html, text, full: html, text
    Fixed example DDF entry. Redmine #6626.
• src/hg/encode/DAFs/3.0/hg19/wgEncodeUchicagoTfbs.daf
  • lines changed 1, context: html, text, full: html, text
    Updated bam validation to be 99.0%. Redmine #5697.
  • lines changed 1, context: html, text, full: html, text
    Forgot to increment the DAF version to 1.4 in previous commit: f84df47051abb23f950f4583df4dffaaa983edf7.
  • lines changed 4, context: html, text, full: html, text
    Updated daf to use 98% bam pass rate and require replicates being tracked for Signal and Peak views. Redmine #5697.
• src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf
  • lines changed 2, context: html, text, full: html, text
    Fixed DAF for bedRnaElements to have sql table reference for loading purposes. Redmine #5986.
  • lines changed 2, context: html, text, full: html, text
    Added lab CSHL-m for mouse transcriptome lab, for reproting purposes. Redmine #5986.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeBroadHistone.release2.notes
  • lines changed 2511, context: html, text, full: html, text
    Added release 2 notes for track. Redmine #4145.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 70, context: html, text, full: html, text
    Added cv items for new repli-seq data from Gilbert lab. Also took the first stab at a DAF for the Human data set. Redmine #6627, #6626.
  • lines changed 75, context: html, text, full: html, text
    Added control specific terms for the eGFP antibodies. Redmine #5697.
  • lines changed 11, context: html, text, full: html, text
    Added lab CSHL-m for mouse transcriptome lab, for reproting purposes. Redmine #5986.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 1141, context: html, text, full: html, text
    Added in metadata and objects that were removed using old revoke policy to follow new revoke policy. Also updated md5sums. Redmine #4145, note #26.
  • lines changed 227, context: html, text, full: html, text
    Updated fileName to have .bai file and added md5sums. Redmine #4145.
  • lines changed 577, context: html, text, full: html, text
    Added expId's and accessioned experiments new for release 2. Redmine #4145.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUmassDekker5C.ra
  • lines changed 773, context: html, text, full: html, text
    Added in full set of files for track from submission 5451. Redmine #225
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Added a third release of track that moved over the A549 and Monocytes CD14 data sets into it, to mantain a clean version of Release 2. Redmine #4145, #6919.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.html
  • lines changed 12, context: html, text, full: html, text
    Updated Release notes for track. Redmine #4145.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.ra
  • lines changed 180, context: html, text, full: html, text
    Added a third release of track that moved over the A549 and Monocytes CD14 data sets into it, to mantain a clean version of Release 2. Redmine #4145, #6919.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.ra
  • lines changed 4206, context: html, text, full: html, text
    Added a third release of track that moved over the A549 and Monocytes CD14 data sets into it, to mantain a clean version of Release 2. Redmine #4145, #6919.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra
  • lines changed 2, context: html, text, full: html, text
    Commented out color and type lines for wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalMinusRawRep1 which seem to be comming from subId 4061. The lines were breaking the make. Redmine #1634.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra
  • lines changed 33, context: html, text, full: html, text
    Added in treatment subGroups for track that were missing in commit: 840a873d9180863c4a6a015cf33d8b8c52b50a10. Redmine #4143.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.ra
  • lines changed 55, context: html, text, full: html, text
    Added in full set of files for track from submission 5451. Redmine #225
  • lines changed 1, context: html, text, full: html, text
    Updated the scoreFilter to be default 0. Redmine #225.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.html
  • lines changed 14, context: html, text, full: html, text
    Fixes for Redmine #4577 4. Replaced semicolon with comma between cell line and replicate 5. Replaced comma with semicolon before G1/G1b list in description section 6. Removed comma after G2 in description section 7 .Removed comma after Percetage-Normalized Signal in descrption section 8. Removed comma after Peaks in description section 9. Removed comma after Valleys in description section 10. Removed hyphen between weighted average 11. Italicized in vivo 12. Removed semicolons and made 3 seperate sentences in long section of first paragrah in methods section 13 Broke up long on going sentence in last paragraph of Methods section 15. Updated references to be to NCBI Pubmed. 16. Updated Long labels to be consitent and use Repli-seq instead of Replication Timing
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Fixes for Redmine #4577 1. Changed alphabetical order of HeLa-S3 and HepG2 2. Changed alphabetical order of BJ and BGO2ES
  • lines changed 32, context: html, text, full: html, text
    Fixes for Redmine #4577 4. Replaced semicolon with comma between cell line and replicate 5. Replaced comma with semicolon before G1/G1b list in description section 6. Removed comma after G2 in description section 7 .Removed comma after Percetage-Normalized Signal in descrption section 8. Removed comma after Peaks in description section 9. Removed comma after Valleys in description section 10. Removed hyphen between weighted average 11. Italicized in vivo 12. Removed semicolons and made 3 seperate sentences in long section of first paragrah in methods section 13 Broke up long on going sentence in last paragraph of Methods section 15. Updated references to be to NCBI Pubmed. 16. Updated Long labels to be consitent and use Repli-seq instead of Replication Timing
  • lines changed 1, context: html, text, full: html, text
    Fixed issues in Redmine #4577 18. Fixed spelling of header in hgFileUi for Phase from Hase
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 902, context: html, text, full: html, text
    Added Contigs and TranscripDeNovo views. Also updated the configuration page and hgFileUi. Redmine #5986.
  • lines changed 239, context: html, text, full: html, text
    Added lab CSHL-m for mouse transcriptome lab, for reproting purposes. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.ra
  • lines changed 1, context: html, text, full: html, text
    Removed incorrect 2 on long label.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.html
  • lines changed 3, context: html, text, full: html, text
    Added Contigs and TranscripDeNovo views. Also updated the configuration page and hgFileUi. Redmine #5986.
  • lines changed 1, context: html, text, full: html, text
    Fixed hardcoded link to relative link. Redmin #6526.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.ra
  • lines changed 162, context: html, text, full: html, text
    Added Contigs and TranscripDeNovo views. Also updated the configuration page and hgFileUi. Redmine #5986.
  • lines changed 27, context: html, text, full: html, text
    Forgot submittions 5439 in data load. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
  • lines changed 41, context: html, text, full: html, text
    Updated longLabels to fix inconsistency found in QA process. Redmine #110.