Commits for vsmalladi

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

• 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/wgEncodeLicrHistone.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra - lines changed 4, context: html, text, full: html, text
• Used rewording from LICR Histone track description provide by Vanessa to make it more readable.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html - lines changed 6, 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.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra - lines changed 4, context: html, text, full: html, text
• Added 2 new protocols provided by Myers lab.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 10, context: html, text, full: html, text
• Added 2 new views plus and minus raw signal for Strand specific signal.
  • src/hg/encode/DAFs/2.0/uwMm9RnaSeq.daf - lines changed 14, context: html, text, full: html, text
• Added age 18.5 for submission presented by UW for their RNA-seq submissions.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 7, context: html, text, full: html, text
• Updated Reference ordering to be alphabetically. Redmine 191, note #26.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.html - lines changed 12, 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.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html - lines changed 9, 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.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html - lines changed 14, 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.html - lines changed 4, context: html, text, full: html, text
• Removed treatment in fileSortOrder, this is not relevant for this track. Redmine 3629, note 10.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.ra - lines changed 1, 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/wgEncodeLicrRnaSeq.ra - lines changed 20, context: html, text, full: html, text
• Added 5 cell types, 1 strain and 2 new ages.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 109, context: html, text, full: html, text
• Added the Thymus protocol for the Stam lab.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Updated bam validation to be 5 mismatches and 99.9% of bam complies.
  • src/hg/encode/DAFs/2.0/uwMm9RnaSeq.daf - lines changed 2, context: html, text, full: html, text