File Changes for vsmalladi

v250_base to v251_preview (2011-04-19 to 2011-04-26) v251

• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUchicagoTfbs.release1.notes
  • lines changed 21, context: html, text, full: html, text
    Added files, which are symbolic links to the same file, for inputcontrol rep 1 which is shared by all experiments. Removed the Initial file name and added the 6 duplicates of the file for each experiment.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 81, context: html, text, full: html, text
    Added 4 cell lines and 2 strains. Updated the catergory for 2 cell lines
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 3, context: html, text, full: html, text
    Correct meta-data for fastq for Sl14 and SL167.
  • lines changed 25, context: html, text, full: html, text
    Updated protocol for wgEncodeHaibTfbsGm12892ControlV0416101AlnRep1 to match CV. Removed wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep2 from submission 3877, which had wrong meta-data and was advised by lab they would like me to revoke.
  • lines changed 33, context: html, text, full: html, text
    Added 4 missing or updated files to complete experiments.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 24, context: html, text, full: html, text
    Removed fileIndex reference from meta-data.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 445, context: html, text, full: html, text
    Removed fileIndex reference from meta-data.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra
  • lines changed 276, context: html, text, full: html, text
    Input Control Replicate 1 was used as control for all Replicate 1's for each experiment. To correctly assign experiment Id's and groupings renamed the wgEncodeUchicagoTfbsK562InputControl*Rep1 files as wgEncodeUchicagoTfbsK562InputControlfos*Rep1. Then made symbolic links for all other experiments to wgEncodeUchicagoTfbsK562InputControlfos*Rep1 files following naming convention of inputs for replicate 2's. Added meta-data for this Rep1 input controls for each experiment. Also updated meta-data of control names for peaks and signals to explicitly state the control pairing used. Removed control as a sortable field in trackDb.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 6, context: html, text, full: html, text
    Removed fileIndex reference from meta-data.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 77, context: html, text, full: html, text
    Removed fileIndex reference from meta-data.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 67, context: html, text, full: html, text
    Removed fileIndex reference from meta-data.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.html
  • lines changed 49, context: html, text, full: html, text
    Added Display Conventions section. Updated contacts to be more inline with labs initial track description. Updated References to be link.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.ra
  • lines changed 13, context: html, text, full: html, text
    Input Control Replicate 1 was used as control for all Replicate 1's for each experiment. To correctly assign experiment Id's and groupings renamed the wgEncodeUchicagoTfbsK562InputControl*Rep1 files as wgEncodeUchicagoTfbsK562InputControlfos*Rep1. Then made symbolic links for all other experiments to wgEncodeUchicagoTfbsK562InputControlfos*Rep1 files following naming convention of inputs for replicate 2's. Added meta-data for this Rep1 input controls for each experiment. Also updated meta-data of control names for peaks and signals to explicitly state the control pairing used. Removed control as a sortable field in trackDb.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 194, context: html, text, full: html, text
    Added submissoin 3920 and 3921. Sub 3921 replaced 3275.
  • lines changed 261, context: html, text, full: html, text
    Added missing input signals for Heart and Kidney.
  • lines changed 287, context: html, text, full: html, text
    Added Lung experiments.
  • lines changed 287, context: html, text, full: html, text
    Added CTCF and input experiments for Liver.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 4, context: html, text, full: html, text
    Removed fileIndex reference from meta-data.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 24, context: html, text, full: html, text
    Removed fileIndex reference from meta-data.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 2, context: html, text, full: html, text
    Fixed term error: 0 adult-8wks to be age adult-8wks.
  • lines changed 12, context: html, text, full: html, text
    Removed fileIndex, as this metaData var is being phased out.
  • lines changed 1322, context: html, text, full: html, text
    Add 12 submissions. Some were attic that I currently handheld into the proper metadata and handling in trackDb.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra
  • lines changed 10, context: html, text, full: html, text
    Added submissoin 3920 and 3921. Sub 3921 replaced 3275.
  • lines changed 18, context: html, text, full: html, text
    Added missing input signals for Heart and Kidney.
  • lines changed 27, context: html, text, full: html, text
    Added Lung experiments forgot the trackDb.ra
  • lines changed 27, context: html, text, full: html, text
    Added CTCF and input experiments for Liver.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra
  • lines changed 342, context: html, text, full: html, text
    Add 12 submissions. Some were attic that I currently handheld into the proper metadata and handling in trackDb.
  • lines changed 1, context: html, text, full: html, text
    Added fileSortOrder in trackDb to display new downlaods page.