Commits for vsmalladi

v250_preview2 to v250_base (2011-04-12 to 2011-04-19) v250

• Updated tracks on hg19 and hg18 to have correct meta-data for IRF4, EBF and HA-F2F1 antibodies. IRF4 and EBF were acceptiable previously, however they were duplicated and subsequently retired as EBF1_(SC-137065) and IRF4_(SC-6059) were used in hg19. As a result needed to rename the wgEncodeSydhTfbsGm12878EbfStd experiment tables and files to match the correct EBF1 tag. Updated all meta-data on hg18 and hg19. The HA-F2F1 antibody was incorrectly named and should be HA-E2F1, which was corrected. Re-ran mdbPrint -validate to verify that all antibodies are correct. Lastly, updated the lab UCD(Farnham) -> UCD which is in the cv.ra .
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 30, context: html, text, full: html, text
• Fixed incorrect lab name for mouse track as Stanford -> Stanford-m
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 43, context: html, text, full: html, text
• When changing the metaData, file and table names for EBF -> EBF1_(SC-137065), I forgot to add the changes to trackDb file.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 9, context: html, text, full: html, text
• Added support for tissueSource to be tracked for pooled and individual animals in meta-data.
  • src/hg/encode/encodeValidate/config/fields.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 22, context: html, text, full: html, text
• Removed metaobject wgEncodeSydhTfbsHuvecInputUcdAlnRep1 since bam were trying to be concatenated in submission 1207 and the bam never seemed to have loaded.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 22, context: html, text, full: html, text
• Merge branch 'master' into PooledTissue
• Added new DDF term tissueSourceType to capture the act of pooling mouse tisses or the use of an individual mouse for an experiment.
  • src/hg/encode/encodeValidate/config/fields.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 6, context: html, text, full: html, text
• Added tissueSourceType meta-data for the UW lab for 20 experiments.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 101, context: html, text, full: html, text
• Added 9 submissions to 2 tracks. Included 5 resubmissions of tracks with updated data(Signals, peaks).
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 765, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 199, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra - lines changed 109, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra - lines changed 55, context: html, text, full: html, text
• Merge branch 'master' into Development-Mouse
• Added two new data type daf for Mouse UW (DGF and Chip-Seq, TFBS). Also upadted DAFs to keep track of the pooling of tissue samples using new term tissueSourceType.
  • src/hg/encode/DAFs/2.0/uwMm9DnaseDgf.daf - lines changed 82, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/uwMm9DnaseSeq.daf - lines changed 4, context: html, text, full: html, text
  • src/hg/encode/DAFs/2.0/uwMm9Tfbs.daf - lines changed 69, context: html, text, full: html, text
• Removed replicate 3's as adivsed by lab. And updated metaData for Input for TFBS data for resubmitted data.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 60, context: html, text, full: html, text
• Changed Harvard(Weissman) -> Yale(Weissman) to be more accurate.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 49, context: html, text, full: html, text
• Changed Yale(Weissman) -> Yale-Weissman to follow naming convention.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 49, context: html, text, full: html, text
• Forgot to add cv changes: Changed Yale(Weissman) -> Yale-Weissman to follow naming convention.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Added 2 submissions for the TFBS track.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 313, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra - lines changed 37, context: html, text, full: html, text
• Added the first 2 submissions of RNA-seq for Mouse from Stanford/Yale.
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.ra - lines changed 92, context: html, text, full: html, text
• Forgot to add the meta-data for the new Sydh RNA-seq track.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra - lines changed 125, context: html, text, full: html, text
• removed release tag alphas in tracks. Also updated spacing of trackDb.ra files to be sperated by tabs and not white spaces.
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra - lines changed 100, context: html, text, full: html, text
• Added meta-data for Sydh RNA-seq in make file so that meta-data would be visible when alpha was made.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile - lines changed 2, context: html, text, full: html, text
• Added release 2 notes. Also updated windowingFunction from maximum -> mean+whiskers.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.html - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra - lines changed 1, context: html, text, full: html, text
• Added missing files, submission 3877.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 469, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra - lines changed 68, context: html, text, full: html, text
• Merge branch 'master' into Development
• Added 3 submissions of lung Tissue data.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 313, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 157, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra - lines changed 19, context: html, text, full: html, text
• Updated replicate for T-Naive to be replicate 2. redime #2985
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra - lines changed 12, context: html, text, full: html, text
• Updated tissueSourceType for the wgEncodeUwDnaseTnaiveC57bl6MAdult8wks Rep2 experiments.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 7, context: html, text, full: html, text