File Changes for vsmalladi

v253_preview2 to v253_base (2011-06-21 to 2011-06-28) v253

• src/hg/encode/DAFs/2.0/uwMm9RnaSeq.daf
  • lines changed 14, context: html, text, full: html, text
    Added 2 new views plus and minus raw signal for Strand specific signal.
  • lines changed 2, context: html, text, full: html, text
    Updated bam validation to be 5 mismatches and 99.9% of bam complies.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 10, context: html, text, full: html, text
    Added 2 new protocols provided by Myers lab.
  • lines changed 7, context: html, text, full: html, text
    Added age 18.5 for submission presented by UW for their RNA-seq submissions.
  • lines changed 109, context: html, text, full: html, text
    Added 5 cell types, 1 strain and 2 new ages.
  • lines changed 1, context: html, text, full: html, text
    Added the Thymus protocol for the Stam lab.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html
  • lines changed 9, context: html, text, full: html, text
    Added periods (.) after Journal title for all references. Also removed 'the' before darker in Peak description. Redmine 101, note 23, 24.
  • lines changed 14, context: html, text, full: html, text
    Added primary contact as Yin Shen with email address. Removed extra space in hyperlink for Bing Ren's labratory. Also removed periods (.) after article tile in hyperlink. Redmine 101, note 26,27.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra
  • lines changed 4, context: html, text, full: html, text
    Updated both tracks with correct range for Signals for Peaks as well as add a score filter and Shading percentage at 11%. User can now update grey scale of peaks to be darker in browswer. Redmine 975, note 17.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.html
  • lines changed 6, context: html, text, full: html, text
    Added primary contact as Yin Shen with email address. Removed extra space in hyperlink for Bing Ren's labratory. Also removed periods (.) after article tile in hyperlink. Redmine 101, note 26,27.
  • lines changed 4, context: html, text, full: html, text
    Moved periods (.) after article names out of hyper link. Redmine 3629, note 9.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Removed treatment in fileSortOrder, this is not relevant for this track. Redmine 3629, note 10.
  • lines changed 20, context: html, text, full: html, text
    Track checkboxes are either fully filled in or empty. Removed the grayed out checkboxes for Alignments view. View was hidden by default, but subtracks where on. Redmine 3629, note 15.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html
  • lines changed 6, context: html, text, full: html, text
    Used rewording from LICR Histone track description provide by Vanessa to make it more readable.
  • lines changed 9, context: html, text, full: html, text
    Added periods (.) after Journal title for all references. Also removed 'the' before darker in Peak description. Redmine 101, note 23, 24.
  • lines changed 14, context: html, text, full: html, text
    Added primary contact as Yin Shen with email address. Removed extra space in hyperlink for Bing Ren's labratory. Also removed periods (.) after article tile in hyperlink. Redmine 101, note 26,27.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra
  • lines changed 4, context: html, text, full: html, text
    Updated both tracks with correct range for Signals for Peaks as well as add a score filter and Shading percentage at 11%. User can now update grey scale of peaks to be darker in browswer. Redmine 975, note 17.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.html
  • lines changed 12, context: html, text, full: html, text
    Updated Reference ordering to be alphabetically. Redmine 191, note #26.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra
  • lines changed 4, context: html, text, full: html, text
    Updated score range to be 100:1000 for Peaks and HotSpots to match actuall values. Updated Score filter to be min of 100, just as befor min was 500 and score filter was set to 500. Redmine #191 note 23.