File Changes for cricket

v256_base to v257_preview (2011-08-29 to 2011-09-06) v257

• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release2.notes
  • lines changed 424, context: html, text, full: html, text
    dealt with fastqs and wrong error messages
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhRnaSeq.release1.notes
  • lines changed 6, context: html, text, full: html, text
    Reran the make change notes as there were so many difficulites
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 11, context: html, text, full: html, text
    removing the term run
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.new.ra
  • lines changed 1, context: html, text, full: html, text
    Removing the UCSC accession column for an hg18 track
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 9, context: html, text, full: html, text
    Removing V2 that were not really V2, there never was a V1
  • lines changed 5, context: html, text, full: html, text
    One more file that says V2 when there was never a V1
  • lines changed 1195, context: html, text, full: html, text
    Added back the 50 bigwigs that were replaced and are on the RR
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
  • lines changed 397, context: html, text, full: html, text
    Adding new data and pulling old data
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
  • lines changed 287, context: html, text, full: html, text
    Adding 13 new cell lines to this composite
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 8, context: html, text, full: html, text
    Getting rid of Astrocy
  • lines changed 139, context: html, text, full: html, text
    Changing astrocy to NH-A
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.ra
  • lines changed 21, context: html, text, full: html, text
    Changing the Tier 1 and Tier 2 cells to have 1 and 2 before the tag
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSc.html
  • lines changed 105, context: html, text, full: html, text
    Basic track description outline for new Single Cell RNA Seq track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
  • lines changed 34, context: html, text, full: html, text
    adding new views
  • lines changed 118, context: html, text, full: html, text
    Adding new data and pulling old data
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra
  • lines changed 7, context: html, text, full: html, text
    Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 94, context: html, text, full: html, text
    Changing labels to have clone-fee clone-based
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
  • lines changed 13, context: html, text, full: html, text
    Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.ra
  • lines changed 1, context: html, text, full: html, text
    removing Astrocy
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
  • lines changed 123, context: html, text, full: html, text
    Adding 13 new cell lines to this composite
  • lines changed 1, context: html, text, full: html, text
    removing Astrocy
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
  • lines changed 14, context: html, text, full: html, text
    Getting rid of Astrocy
  • lines changed 3, context: html, text, full: html, text
    Standardizing the cell line labels so that they play well with encodePatchTdb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Removing Astrocy
  • lines changed 3, context: html, text, full: html, text
    Changing the Tier 1 and Tier 2 cells to have 1 and 2 before the tag
  • lines changed 3, context: html, text, full: html, text
    These were checked in prematurely before with the tags changed, they are fixed now.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.new.ra
  • lines changed 60, context: html, text, full: html, text
    Standardizing the cell line labels so that they play well with encodePatchTdb
  • lines changed 11, context: html, text, full: html, text
    Changing the Tier 1 and Tier 2 cells to have 1 and 2 before the tag
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.new.ra
  • lines changed 22, context: html, text, full: html, text
    Standardizing the cell line labels so that they play well with encodePatchTdb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.new.ra
  • lines changed 31, context: html, text, full: html, text
    Standardizing the cell line labels so that they play well with encodePatchTdb
  • lines changed 1, context: html, text, full: html, text
    Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.html
  • lines changed 11, context: html, text, full: html, text
    Addressing Jacobs concerns #2020
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
  • lines changed 2, context: html, text, full: html, text
    Addressing Jacobs concerns #2020
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.ra
  • lines changed 19, context: html, text, full: html, text
    Changing the Tier 1 and Tier 2 cells to have 1 and 2 before the tag
  • lines changed 9, context: html, text, full: html, text
    These were checked in prematurely before with the tags changed, they are fixed now.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 25, context: html, text, full: html, text
    Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
  • lines changed 5, context: html, text, full: html, text
    These were checked in prematurely before with the tags changed, they are fixed now.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.ra
  • lines changed 39, context: html, text, full: html, text
    Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.ra
  • lines changed 3, context: html, text, full: html, text
    Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.html
  • lines changed 6, context: html, text, full: html, text
    Added the SAM explaination and fixed Farhnam reference
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    The view limits are set to 10
  • lines changed 9, context: html, text, full: html, text
    Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.ra
  • lines changed 13, context: html, text, full: html, text
    Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra
  • lines changed 8, context: html, text, full: html, text
    Standardizing the cell line labels so that they play well with encodePatchTdb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
  • lines changed 8, context: html, text, full: html, text
    Standardizing the cell line labels so that they play well with encodePatchTdb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.ra
  • lines changed 10, context: html, text, full: html, text
    Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
• src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.ra
  • lines changed 9, context: html, text, full: html, text
    Trying out the new labeling
  • lines changed 136, context: html, text, full: html, text
    Standardizing labels for Tier1 and Tier2 so that encodePatchTDB works
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Fixing the snpDb error for Angie