File Changes for vsmalladi

v258_preview2 to v258_base (2011-10-04 to 2011-10-10) v258

• src/hg/encode/DAFs/3.0/mm9/wgEncodeCaltechRnaSeq.daf
  • lines changed 71, context: html, text, full: html, text
    Added newest version of Caltech RNA-seq DAF.
  • lines changed 3, context: html, text, full: html, text
    Updated DAF for new bam validation and compliance of views with cv.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhHistone.release2.notes
  • lines changed 362, context: html, text, full: html, text
    Updated Release Notes for track. This includes adding old files and tables that were removed. Redmine #4018.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUw5C.release1.notes
  • lines changed 3, context: html, text, full: html, text
    Fixes issues in Redmine #222 1. Added the dummy table, wgEncodeUw5C to composite level metaData and added table 'by hand' to notes file 2. There is no whole-chromosome analysis as of yet. So I will commented that section for now and highlight the two other projects. 3. Updated the setnece "(Neuroblastoma cell line differentiated with retinoic acid, aka SKNSH)." -> "Updated sentence to be (neuroblastoma cell line differentiated, SKNSH, with retinoic acid)." 4. Fixed indenting to be the same for description of each view. 5. Moved the following waring to matrix view "In order to understand the Matrix data, you must download the associated primer data file." 6. Added link to cell growth protocols 7. Reordered the following sentence:"The interaction files provided map all the reads in the output sequence without a mismatch threshold." 8. Changed 2 -> Two in the following sentence: "2 replicates were performed ..." 9. Added space after greater than symbol for 'extending > 2 Mb' 10. Added space after greater than symbol for 'displaying correlation coefficient > 0.9' 11. No need for release notes for the first release. Removed this section 12. Removed extra <p> and paired up <p> with </p>
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 20, context: html, text, full: html, text
    Updated Treatments to be descriptive of the exact treatment used and not the differentiation state and treatment. Redmine #3733.
  • lines changed 10, context: html, text, full: html, text
    Updated metadata to used region as an experiment defining variable. Restoring CV terms that were previously deperated in Redmine #222. There will be 11 experiments. Redmine #222.
  • lines changed 1, context: html, text, full: html, text
    These changes are related to QA fixes of this track. Redmine #4018 1. Changed label in matrix from 1K562 -> K562 2. Updated Peaks to be default pack 3. Greyed check boxes were fixed once Peak view was set from default hide->peak 4. Turned off Peaks configuration box 5. Updated long and short labels for 4 track that were autogenerated by pipeline 6. Updated Release Notes section to have date and states that new experiments were added 7. In Methods section of track Description changed 300-500bp -> 300-500 bp 8. Added comma after phrase Also included for each cell type 9. Split the following sentence into 2 sentences: Peaks and signals displayed in this track are the results of pooled replicate sequence and alignment files for each replicate are available for download. This should be two sentences. 10. Updated the description in cv and track to state NTera-2 instead of Ntera2. Also in track description added name for what we call cell line. 11. Updated Reference link for Using ChIP-Seq Technology to Generate High-Resolution Profiles of... 13 In References updated _BLANK to have quotes around it 14. Removed spaces for the following reference: 2011; 6(2): e17121.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 7, context: html, text, full: html, text
    Added fake subId for CRG Alignability data for Kate's reporting.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    Updated file name for obj wgEncodeRegTfbsCells from wgEncodeRegTfbsCells.tab.gz -> wgEncodeRegTfbsClusteredCells.tab.gz. Fixes Redmine #5513.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 724, context: html, text, full: html, text
    Added back 27 files that were renamed from k562b -> k562 between release 1 and 2. Following new release policy.
  • lines changed 17, context: html, text, full: html, text
    Added md5sum for PANC-1 files that didn't have that information and lacked the .bam.bai in the fileName list. Redmine #4018. Note 46.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUw5C.ra
  • lines changed 78, context: html, text, full: html, text
    Updated metadata to used region as an experiment defining variable. Restoring CV terms that were previously deperated in Redmine #222. There will be 11 experiments. Redmine #222.
  • lines changed 2, context: html, text, full: html, text
    Fixes issues in Redmine #222 1. Added the dummy table, wgEncodeUw5C to composite level metaData and added table 'by hand' to notes file 2. There is no whole-chromosome analysis as of yet. So I will commented that section for now and highlight the two other projects. 3. Updated the setnece "(Neuroblastoma cell line differentiated with retinoic acid, aka SKNSH)." -> "Updated sentence to be (neuroblastoma cell line differentiated, SKNSH, with retinoic acid)." 4. Fixed indenting to be the same for description of each view. 5. Moved the following waring to matrix view "In order to understand the Matrix data, you must download the associated primer data file." 6. Added link to cell growth protocols 7. Reordered the following sentence:"The interaction files provided map all the reads in the output sequence without a mismatch threshold." 8. Changed 2 -> Two in the following sentence: "2 replicates were performed ..." 9. Added space after greater than symbol for 'extending > 2 Mb' 10. Added space after greater than symbol for 'displaying correlation coefficient > 0.9' 11. No need for release notes for the first release. Removed this section 12. Removed extra <p> and paired up <p> with </p>
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html
  • lines changed 12, context: html, text, full: html, text
    Fixes issues related to Redmine #43: 1. a. changed 'generate' -> 'generated' b. updated words in the following sentence 'They contain information about human RNAs > 200 nucleotides in length obtained as short reads off the Illumina GAIIx platform.' -> 'They contain information about human RNAs > 200 nucleotides in length that were obtained as short reads from the Illumina GAIIx platform.' c. since data is plural updated the sentence: '...there is also data from various subcellular...' -> '...there are also data from various...' 2. Changed 2 instances of RNA-Seq -> RNA-seq 3. Removed 4 instances of first person and changed to third person passive 4. Removed pubmed id in link and used the procotol name to link to the paper.
  • lines changed 5, context: html, text, full: html, text
    Fixes for Redmine #43 1. Changed external links to internal links for data from same biological replicates. GIS RNA-PET is a link to genome-preview since this is not released yet, the rest are relative links. 2. Changed is -> are since data is plural in the following sentence:"Data is available from biological replicates of several cell lines"
  • lines changed 7, context: html, text, full: html, text
    Fixes for Redmine #43 1. Updated hypertext link for STAR information to be Gineras lab, instead of actual url. 2. Updated wording in the sentence about threshold to make it clear that the user should use the threshold. Changed "The IDR values for each element are included in the files for end-users to threshold on." -> "The IDR values for each element are included in the files for end-users to use as a threshold." 3. Fixed spelling of explanation 4. Fixed double the's "... the the ..." 5. Fixed spelling of signals 6. Fixed spelling of available.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.html
  • lines changed 1, context: html, text, full: html, text
    Added description of the tag XA. Redmine #42.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.html
  • lines changed 12, context: html, text, full: html, text
    These changes are related to QA fixes of this track. Redmine #4018 1. Changed label in matrix from 1K562 -> K562 2. Updated Peaks to be default pack 3. Greyed check boxes were fixed once Peak view was set from default hide->peak 4. Turned off Peaks configuration box 5. Updated long and short labels for 4 track that were autogenerated by pipeline 6. Updated Release Notes section to have date and states that new experiments were added 7. In Methods section of track Description changed 300-500bp -> 300-500 bp 8. Added comma after phrase Also included for each cell type 9. Split the following sentence into 2 sentences: Peaks and signals displayed in this track are the results of pooled replicate sequence and alignment files for each replicate are available for download. This should be two sentences. 10. Updated the description in cv and track to state NTera-2 instead of Ntera2. Also in track description added name for what we call cell line. 11. Updated Reference link for Using ChIP-Seq Technology to Generate High-Resolution Profiles of... 13 In References updated _BLANK to have quotes around it 14. Removed spaces for the following reference: 2011; 6(2): e17121.
  • lines changed 3, context: html, text, full: html, text
    Forgot 13. In References updated _BLANK to have quotes around it, in last commit.
  • lines changed 1, context: html, text, full: html, text
    Fixed overhanging period in link. Redmine #4018. Note #42.
  • lines changed 4, context: html, text, full: html, text
    Updated hyperlinks to not expose the url but to have human readable text. Redmine #4018.
  • lines changed 7, context: html, text, full: html, text
    Fixed hyperlinks to be on 'Chip and Library Protocol' and 'detailed protocol' instead of the institute. Redmine #4018.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.ra
  • lines changed 15, context: html, text, full: html, text
    These changes are related to QA fixes of this track. Redmine #4018 1. Changed label in matrix from 1K562 -> K562 2. Updated Peaks to be default pack 3. Greyed check boxes were fixed once Peak view was set from default hide->peak 4. Turned off Peaks configuration box 5. Updated long and short labels for 4 track that were autogenerated by pipeline 6. Updated Release Notes section to have date and states that new experiments were added 7. In Methods section of track Description changed 300-500bp -> 300-500 bp 8. Added comma after phrase Also included for each cell type 9. Split the following sentence into 2 sentences: Peaks and signals displayed in this track are the results of pooled replicate sequence and alignment files for each replicate are available for download. This should be two sentences. 10. Updated the description in cv and track to state NTera-2 instead of Ntera2. Also in track description added name for what we call cell line. 11. Updated Reference link for Using ChIP-Seq Technology to Generate High-Resolution Profiles of... 13 In References updated _BLANK to have quotes around it 14. Removed spaces for the following reference: 2011; 6(2): e17121.
  • lines changed 1, context: html, text, full: html, text
    Added controlId and geoSampleAccession columns to hgFileUi. Redmine #4018.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.html
  • lines changed 46, context: html, text, full: html, text
    Fixes issues in Redmine #222 1. Added the dummy table, wgEncodeUw5C to composite level metaData and added table 'by hand' to notes file 2. There is no whole-chromosome analysis as of yet. So I will commented that section for now and highlight the two other projects. 3. Updated the setnece "(Neuroblastoma cell line differentiated with retinoic acid, aka SKNSH)." -> "Updated sentence to be (neuroblastoma cell line differentiated, SKNSH, with retinoic acid)." 4. Fixed indenting to be the same for description of each view. 5. Moved the following waring to matrix view "In order to understand the Matrix data, you must download the associated primer data file." 6. Added link to cell growth protocols 7. Reordered the following sentence:"The interaction files provided map all the reads in the output sequence without a mismatch threshold." 8. Changed 2 -> Two in the following sentence: "2 replicates were performed ..." 9. Added space after greater than symbol for 'extending > 2 Mb' 10. Added space after greater than symbol for 'displaying correlation coefficient > 0.9' 11. No need for release notes for the first release. Removed this section 12. Removed extra <p> and paired up <p> with </p>
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.html
  • lines changed 9, context: html, text, full: html, text
    Fixes for track. Redmine #4460.1. Removed extra quotation mark 2. Update false discovery percent to be spelled out 3. Added space between > and 0.9. The greater than symbol is html compliant. 4. Changed Release Month to be October. 5. Removed numeric indication of number of experiments and state experiments were added. 6. Added miss closing paragraph tags 12)Moved the closing tag from after list in Release Notes to before list in release notes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
  • lines changed 2, context: html, text, full: html, text
    Updated tag for WI38 hydroxytamoxifen to go from WI30 -> WI38. Removed Treatment column as this is redundant since this is collapsed in the Cell Label.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechHist.ra
  • lines changed 72, context: html, text, full: html, text
    Added controlId as a number that corresponds to the labExpId of the given control experiment. Also update control for 2 Experiments that had stated None but were Control 32bp.
  • lines changed 127, context: html, text, full: html, text
    Updated treatment to be descriptive of what the was actually done to the cells. Moved cell state into cell version. THIS IS A TRIAL. Redmine #3733, note #40.
  • lines changed 575, context: html, text, full: html, text
    Updated Treatments to be descriptive of the exact treatment used and not the differentiation state and treatment. Redmine #3733.
  • lines changed 21, context: html, text, full: html, text
    Updated Obj names to have control in them for objs that failed to have control.
  • lines changed 6, context: html, text, full: html, text
    Added expVars and composite metadata.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechTfbs.ra
  • lines changed 121, context: html, text, full: html, text
    Added controlId as a number that corresponds to the labExpId of the given control experiment. Also update control for 2 Experiments that had stated None but were Control 32bp.
  • lines changed 241, context: html, text, full: html, text
    Updated treatment to be descriptive of what the was actually done to the cells. Moved cell state into cell version. THIS IS A TRIAL. Redmine #3733, note #40.
  • lines changed 819, context: html, text, full: html, text
    Updated Treatments to be descriptive of the exact treatment used and not the differentiation state and treatment. Redmine #3733.
  • lines changed 68, context: html, text, full: html, text
    Added expVars and composite metadata and renamed obj that was missed in initial rename.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 6, context: html, text, full: html, text
    Added expVars and composite metadata.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.ra
  • lines changed 3, context: html, text, full: html, text
    Updated 'Shade of lowest-scoring items' to be 55%. Also updated Signal View range 0:1 and removed individual configuration of Signal Sub-tracks.
  • lines changed 4, context: html, text, full: html, text
    Removed Protocol has a dimension, as this is not a major variable changing in the track.
  • lines changed 9, context: html, text, full: html, text
    Added controlId as a number that corresponds to the labExpId of the given control experiment. Also update control for 2 Experiments that had stated None but were Control 32bp.
  • lines changed 10, context: html, text, full: html, text
    Updated dimensions to be treatment x factor because cell line was the same. Also updated defaults for the 2 tracks.
  • lines changed 1, context: html, text, full: html, text
    Updated treatment to be descriptive of what the was actually done to the cells. Moved cell state into cell version. THIS IS A TRIAL. Redmine #3733, note #40.
  • lines changed 88, context: html, text, full: html, text
    Updated Treatments to be descriptive of the exact treatment used and not the differentiation state and treatment. Redmine #3733.
  • lines changed 8, context: html, text, full: html, text
    Updated Obj names to have control in them for objs that failed to have control.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.ra
  • lines changed 3, context: html, text, full: html, text
    Updated 'Shade of lowest-scoring items' to be 55%. Also updated Signal View range 0:1 and removed individual configuration of Signal Sub-tracks.
  • lines changed 4, context: html, text, full: html, text
    Removed Protocol has a dimension, as this is not a major variable changing in the track.
  • lines changed 8, context: html, text, full: html, text
    Updated dimensions to be treatment x factor because cell line was the same. Also updated defaults for the 2 tracks.
  • lines changed 1, context: html, text, full: html, text
    Updated treatment to be descriptive of what the was actually done to the cells. Moved cell state into cell version. THIS IS A TRIAL. Redmine #3733, note #40.
  • lines changed 170, context: html, text, full: html, text
    Updated Treatments to be descriptive of the exact treatment used and not the differentiation state and treatment. Redmine #3733.
  • lines changed 2, context: html, text, full: html, text
    Added expVars and composite metadata and renamed obj that was missed in initial rename.