File Changes for vsmalladi

v249_preview to v249_preview2 (2011-03-15 to 2011-03-22) v249

• src/hg/encode/DAFs/2.0/stanfordMm9RnaSeq.daf
  • lines changed 60, context: html, text, full: html, text
    First pass of SYDH Mouse RNA-seq DAF.
  • lines changed 1, context: html, text, full: html, text
    Added replicates required at Peak level. Need to confirm with lab if this is correct.
• src/hg/encode/DAFs/2.0/stanfordNucleosome.daf
  • lines changed 12, context: html, text, full: html, text
    Updated DAF settings. Alignments will be download only. Lab will be submitting csfasta and csqual files instead of fastqs. Updated long label for Signal to say Signal instead of Peaks.
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • lines changed 3, context: html, text, full: html, text
    Added strain and age information for know Mouse cell lines.
  • lines changed 3, context: html, text, full: html, text
    Accidently checked in some changes I was playing with. Restoring commig 4888a0b7264461d213f0e0970d4a9fd9b074d983.
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeYaleChIPseq.release4.notes.txt
  • lines changed 1466, context: html, text, full: html, text
    Release notes of release 4 of track.
  • lines changed 1110, context: html, text, full: html, text
    Updated release notes to have path for files.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 18, context: html, text, full: html, text
    Added strain and age information for know Mouse cell lines.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • lines changed 3730, context: html, text, full: html, text
    Removed 2 experiments as they used the wrong lanes (K562: NF-YA and NF-YB). Advised by lab to revoke data from hg18.
  • lines changed 460, context: html, text, full: html, text
    Added release notes to new html file and removed meta-data of replaced files.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Removed 2 experiments as they used the wrong lanes (K562: NF-YA and NF-YB). Advised by lab to revoke data from hg18.
  • lines changed 1, context: html, text, full: html, text
    Removed accession number for wgEncodeUwAffyExonArray track. Accession number has been migrated to metaDb as var=dccInternalNotes. Redmine issue 1492 note 17.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.new.html
  • lines changed 178, context: html, text, full: html, text
    Added release notes to new html file and removed meta-data of replaced files.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.new.ra
  • lines changed 2349, context: html, text, full: html, text
    Removed 2 experiments as they used the wrong lanes (K562: NF-YA and NF-YB). Advised by lab to revoke data from hg18.
  • lines changed 1, context: html, text, full: html, text
    Added release notes to new html file and removed meta-data of replaced files.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 1256, context: html, text, full: html, text
    Undid load of 3 submissions due to meta-data errors: 3752,3751,3749.
  • lines changed 283, context: html, text, full: html, text
    Removed 12 files and meta-data as advised by lab. Redmine issue 3057 note 6.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhNsome.ra
  • lines changed 617, context: html, text, full: html, text
    Reloaded data with normal table and file naming schema, removed docId naming strategy. Also removed fastq files, as these are not the correct RawData format that will be provided by the lab.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 231, context: html, text, full: html, text
    Removed 2 experiments K562 NF-YA and NF-YB the were submitted using incorrect lanes.
  • lines changed 129, context: html, text, full: html, text
    Added submission 3755.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Updated wgEncodeSydhNsome to use global tag's rather than local tags.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 334, context: html, text, full: html, text
    Undid load of 3 submissions due to meta-data errors: 3752,3751,3749.
  • lines changed 1, context: html, text, full: html, text
    Fixed missing underscore(_) in GATA2SC267=GATA2(SC-267)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.html
  • lines changed 90, context: html, text, full: html, text
    Added track description as provided by Peggy Farnham.
  • lines changed 1, context: html, text, full: html, text
    Removed specificiation of human protocols in protocols link.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.ra
  • lines changed 5, context: html, text, full: html, text
    Updated default tracks on to be all cell lines and Histone marks. Updated default signal windowing function to be mean+whiskers.
  • lines changed 4, context: html, text, full: html, text
    Updated spacing of trackDb enteries.
  • lines changed 8, context: html, text, full: html, text
    Updated spacing and removed some extra comment lines.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.ra
  • lines changed 27, context: html, text, full: html, text
    Reloaded data with normal table and file naming schema, removed docId naming strategy. Also removed fastq files, as these are not the correct RawData format that will be provided by the lab.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 20, context: html, text, full: html, text
    Removed 2 experiments K562 NF-YA and NF-YB the were submitted using incorrect lanes.
  • lines changed 21, context: html, text, full: html, text
    Added submission 3755.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 157, context: html, text, full: html, text
    Added 1 submission, subId 3812.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 157, context: html, text, full: html, text
    Added 1 submission, subId 3811.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 1059, context: html, text, full: html, text
    Added 7 new submissions mouse data.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 120, context: html, text, full: html, text
    Renamed 7 replicates as provided by Lab. Redmine issue: 2985.
  • lines changed 51, context: html, text, full: html, text
    Updated UW display with initial attic design for supplemental experiments.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra
  • lines changed 20, context: html, text, full: html, text
    Added 1 submission, subId 3812.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra
  • lines changed 20, context: html, text, full: html, text
    Added 1 submission, subId 3811.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
  • lines changed 127, context: html, text, full: html, text
    Added 7 new submissions mouse data.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra
  • lines changed 85, context: html, text, full: html, text
    Renamed 7 replicates as provided by Lab. Redmine issue: 2985.
  • lines changed 287, context: html, text, full: html, text
    Updated UW display with initial attic design for supplemental experiments.