RR data repushes


Repush Date Initial Push Date Data Database Issue Remedy Engineers
2011-2-14 2011-2-3 Agilent Array track hg19, hg18, mm9, rn4 Bob talked to Anniek at Agilent and they decided the track was better suited to the Variation group. We also changed the name of the track on hg19 in anticipation of adding more tracks to this composite. Redid trackDb. http://redmine.soe.ucsc.edu/issues/1791 Bob, Mary
2011-1-25 2010-11-15 snp131 hg19 This is a correction to one value in one row of snp131: rs75946332 had "" for func, which caused it to be completely omitted from display. Angie set its func to "unknown" because NCBI doesn't make a synon or nonsynon call for it, although from the browser & details page it is clearly a nonsense mutation. Angie also fixed the script loophole that allowed this to happen. Angie, Greg
2010-10-20 2010-11-15 gold felCat4, calJac3 Hiram discovered chromosome names longer than 16 characters hadn't been loaded correctly into the gold table on an initial genome browser build when using hgGoldGapGl. Hiram fixed hgGoldGapGl to load longer chromosome names. Mary repushed the gold table for all assemblies that had chromosome names, which ended up being on felCat4 and calJac3. http://redmine.soe.ucsc.edu/issues/1174 Hiram, Chin, Mary
2010-08-12 2007-08-22 mm8 to mm9 liftOver mm8 User (John Didion jdidion@email.unc.edu) noticed that couldn't lift a section of mm8 to mm9 even though it blatted perfectly. http://redmine.soe.ucsc.edu/forum/index.php?t=rview&goto=312&th=160#msg_312 http://redmine.soe.ucsc.edu/issues/352 Jim, Hiram and Galt noticed that the program used to make same species liftOvers was using 10k chunks rather than 5k chunks, which is the maximum allowed by blat. Galt re-did the program, replaced the download and gbdb file and mary checked and pushed the two files. http://redmine.soe.ucsc.edu/issues/444 Jim, Hiram, Galt, Mary
2009-07-21 2009-06-25 ENCODE Open Chromatin hg18 Terry Furey noticed that the wgEncodeUncFAIREseqPeaksHelas3 table and associated downloads file was missing from the track. Tim noticed that the downloads file was also missing from genome-test. Tim replaced the download file and brooke checked and pushed the table/file. tim, brooke
2009-02-12 2008-09-03 kgColor hg18 The new UCSC Genes build (ucsc.11) added the "ccds" type. The txGeneColor program originally did not take this into account and hence many genes were colored light blue instead of the dark blue. Fan updated txGeneColor.c and re-loaded the kgColor table. fan, brooke
2008-09-23 2007-09-03 knownGenePep hg18 User found 12 non-coding genes that had associated proteins. Jim fixed the process and consequently the table. jim, ann
2008-05-27 2007-07-16 multiz upstream files dm3 The gene names were truncated to 9 characters. Angie fixed it. angie, ann
2008-05-07 2008-08-22 bigZip download files mm9 The chromTrf.tar.gz file had only symlinks in it. Hiram fixed it. hiram, ann
2008-04-01 2008-01-02 Geneid Genes bosTau3 There were some corrupt entries in the table (as downloaded from data source). These were found by Ann's bi-montly joinerCheck run. Hiram contacted the data provider who recreated the table. Hiram reloaded. hiram, ann
2008-02-06 2007-05-19 HapMap SNPs hg17 hapmapAllelesChimp had some incorrect data in chrY and chrY_random, and outdated data on chrM and chr21 -- left over from Feb. 2007 version, in which hg18 liftOver files were used instead of hg18. The panTro2 chroms that do not have quality scores were left out of the June 2007 data correction. Angie regenerated the hapmapAllelesChimp table, as well as the hapmapAllelesSummary table, since hapmapAllelesChimp is used in generating it. angie, brooke
2008-01-02 various /goldenPath/fr2/multiz5way/ensGene.upstream*.maf.gz /goldenPath/oryLat1/multiz5way/ensGene.upstream*.maf.gz /goldenPath/mm8/multiz17way/upstream*.maf.gz /goldenPath/gasAcu1/multiz8way/ensGene.upstream*.maf.gz /goldenPath/ce4/multiz5way/sangerGene.upstream*.maf.gz /goldenPath/mm9/multiz30way/maf/upstream*.maf.gz /goldenPath/hg18/multiz28way/maf/upstream*.maf.gz various Two problems: (1) gene names were truncated to 9 characters, (2) files included rows for both the gene and the genomic. Jim fixed mafFrags to fix problem 2; Hiram fixed mafFrags and build process to fix problem 1. jim/hiram, ann
2007-10-17 2006-08-07 snpArrayAffy6 hg18 Contributor wanted to remove 25,640 recrds that were not for public distribution. I dropped the rows. fan, bob
2007-10-16 2007-07-02 nscanPasaGene, nscanPasaPep hg18 Gene predictions had strange names, like 'temp_model_1.2'. Searching did not work for these names. Both tables were re-loaded with new names. Mark also added search functionality for these tables. markd, brooke
2007-10-08 2006-02-06 stsInfo2, stsAlias hg18 One stsInfo2 record has 6700 otherNames listed instead of 5. The stsAlias table has 20K rows for that accession. never figured out where the 6700 came from, or where the extra 3500 came from. I dropped the offending stsAlias rows and reloaded only the 6 that should have been there. Also changed the stsInfo2.otherNames field for that accession (AFM067XA9) to have only 5 otherNames. archana, bob
2007-10-03 2007-09-25 RGD QTL rn4 Our QA found a duplicate name in the original data. RGD corrected it. Angie fixed the tables. angie, ann
2007-09-07 2006-06-23 Reg Potential 7X hg17, hg18 Several chroms had data that stopped before then end of the chrom Hiram reloaded the updated data, adding data to hg17.chrom4, 8 and 9 and hg18.chr3,4,9,10,20,21. hiram, bob
2007-09-06 2006-04-14 FISH Clones hg18 The reprocessed and fixed BAC Clone information was not re-loaded into the FISH Clones track data Hiram reloaded the updated BAC clone information into the FISH Clones track data. The new table now has 9,305 unique clone names compared to the existing 9,031 unique clone names hiram,archana
2007-07-20 2006-11-20 TFBS Conserved Sites hg18 A user noticed a problem with the processing of this track. Matt changed the algorithm and recreated the track. There are now 626,065 new sites. matt,ann
2007-07-13 various GenBank and RefSeq tracks canFam1,canFam2 Dog was re-classified as Canis lupus familiaris from Canis familiaris, and this caused native refSeqs to align in the xeno refSeqs track. Mark re-aligned everything and re-loaded all genbank-related tables in both dog assemblies. mark,brooke
2007-07-09 various upstream maf files danRer4, dm3, fr2, galGal3, gasAcu1, hg17, hg18, mm8, oryLat1, rn4 There were e-rows in these files and there shouldn't be. Brian grepped out the e-rows completely. The program that creates these files has also been fixed so that this doesn't continue to happen brian,ann
2007-06-25 2007-05-19 HapMap SNPs hg17 Orthologous allele tables were made using hg17 coordinates on the hg18 database. So conversion was from hg18 (but hg17 coords) --> panTro2/rheMac2. Heather re-made three tables: hapmapAllelesChimp, hapmapAllelesMacaque and hapmapAllelesSummary. Conversion was from hg17 --> panTro2/rheMac2. heather,brooke
2007-05-01 2006-07-28 cnpConrad hg17 Error when lifting from hg16 to hg17 coords that caused all items to be drawn as thick lines, instead of thin and thick. Table was reloaded. Now no items with chromStart > thickStart or chromEnd < thickEnd. heather,brooke
2007-02-27 various xxBlastTab tables hg18,hg17,mm8,mm7,rn4 There were many false matches in the "other species" section of the Known Gene details page. Removed the false matches that had been introduced because of the bad matches from the simple blastp best 1 method. galt,ann
2007-01-11 various MGC Details page ("NCBI Clone Validation" section) hg18,hg17,hg16,hg15,
Problem with the way the synthetic mRNAs are handled by the genbank code. This was causing duplicate alignments with strands listed as '+' and '++'. Corrected genbank software and loaded new table (gbMiscDiff). markd,ann
2006-11-20 2005-02-04 tables for TFBS Conserved track hg18 Many sites were missing because the software missed sites where human, mouse and rat aligned like this: human aca-accc; mouse tca-accc; rat tca-accc Corrected software and reloaded tfbsConsSites table. matt,ann
2006-11-06 2005-02-04 tables for TFBS Conserved track hg17 It was based on a newer version of tfbs names that are not yet public domain Reloaded table. hiram,archana
2006-11-03 2006-05-10 files and tables for STS Markers track mm8 Map distances for Genetic and Radiation Hybrid Maps were incorrect. Rebuilt tables and files. hiram,ann
2006-10-23 2006-02-22 upstream*.maf.gz files hg18 Last 3 digits of many refSeq id's were omitted. Remade new files. Repushed files. fan,archana
2006-06-15 2006-08-21 ENCODE UNC FAIRE hg17 Track broken on RR. Data was incorrect. Made new tables. Repushed tables. rachel,ann
2006-06-14 2006-06-16 Human Mutation hg17 Jim found several broken links to the Penn State database. Belinda removed the 'fake' links. Repushed table. belinda,ann
2006-06-14 2006-05-22 FlyBase Noncoding Genes dm2 Many of the miRNAs were accidentally omitted from the original relese Angie rebuilt with a new script which picked up the missing miRNAs angie,ann
2006-06-14 2005-12-22 Dog Chain/Net/LiftOver(canFam2) hg17 The original run omitted the BLASTZ_ABRIDGE_REPEATS parameter Angie re-ran this with better parameters angie,archana
2006-04-27 2006-03-10 17way Conservation and Most Conserved hg17 user noticed there were overlaps in the pairwise alignments pairwise for xenTro1 and tetNig1 were re-run, as was all downstream stuff kate,ann
2006-03-21 2006-03-10 phastCons17way hg17 user noticed that there was a high Conservation score even if only chimp and rhesus sequences included table was rebuilt using --noninformative=rheMac2 kate,kuhn
2006-02-16 2006-02-14 ctgPos rheMac2 some contigs missing due to too restrictive primary key Robert reloaded table with longer primary key. kuhn
2006-02-08 2004-11-16 seq mm5 Mismatches between seq.extFile and extFile.id on dev & rr (not beta!) Repush seq to rr from beta.
2006-02-07 2004-02-09 seq, extFile hg16 Mismatches between seq.extFile and extFile.id. Broken alignment links for track Affy U133. 4 groups of problem data. 3 needed to be deleted on beta/rr, 1 repushed up from dev->beta/rr.
2006-02-07 2001-10-09 rosChr22Dat, sage, sageCounts, sageExp hgFixed Dev had bad table definitions. Beta had extra lines of data in some tables (header). Fix on dev (ISAM->MyISAM), push to beta & rr/mgc to match timestamp.
2006-02-07 2001-12-19 cghNci60Exps hgFixed Place missing data on rr. Dev had bad table definition. Fix on dev (ISAM->MyISAM), repush to beta to match timestamp, and push rr/mgc.
2006-01-31 2004-06-03 ensGtp hg16 Dev had corrected data. Beta and RR still incorrect. pushed. Makedoc noted.
2006-01-30 2005-06-30 Superfamily hg17 Table "superfamily" not released with other sf* tables in June KG push. pushed
2006-01-12 2004-02-14 Chain/Net to anoGam1, droVir1, droMoj1, droYak1 dm2 data was rerun with better blastz parameters repushed.
2006-01-11 2004-09-29 sgpGene galGal2 contributor updated data repushed.
2006-01-11 2005-08-31 encodeEgaspPartAugustusEst hg17 The table was mistakenly loaded. data matched encodeEgaspFullGenemark repushed. kuhn
2006-01-06 2005-May Conservation, Most Conserved, Nets/Chains to hg17, rn3, galGal2 mm6 There was an error in the creation method for the original tables - these fix that error. repushed.
2006-01-03 2005-11-18 ENCODE Uppsala Chip hg17 Contributor noticed they had submitted bad coordinate data. Update data sent to us, loaded, qc'd and repushed.
2005-12-27 2005-05-04 genbank tables mm6 revised by mark with new filtering repushed. kuhn
2005-12-19 2005-03-31 Cow Synteny hg15 revised by contributor. repushed. kuhn
2005-12-16 2004-07-23 genbank tables hg17 revised by mark with new filtering repushed. kuhn
2005-11-07 2005-10-14,
affyTranscription Phase 2 hg17,hg15 Map Box problem in browser window. Fix in cgi release v120.
2005-11-02 2005-07-05 STS Markers mm6 Changed filtering. Remove pairs that were very far apart. Badly formatted rows deleted from all_sts_primer.
2005-10-03 2005-07-15 Evofold hg16,hg17 Changed filtering. Removed non-syntenic predictions and predictions with only 4 pairing bases.
2005-09-16 2005-07-06 ENCODE Stanf Meth Score hg16 2 tables named incorrectly, preventing them from being displayed in browser. Dropped encodeStanfordMethSmoothedJeg3 & encodeStanfordMethSmoothedBe2c. Added encodeStanfordMethSmoothedJEG3 & encodeStanfordMethSmoothedBe2C.
2005-08-02 Affy pVal, Affy RNA Signal, Yale TAR, Yale RNA hg16 Coords needed +1 (both start and end) Reloaded 77 tables.
2005-07-26 2005-07-14 encodeMlaganSummary hg16 Three species (opossum, frog and monkey) were not displaying when zoomed out >1MB. (found at ENCODE data meetings) Reloaded table.
2005-06-15 2004-12-23 Contigs danRer2 Incomplete data load into contigs track table due to primary key conflicts. 4,415 additional contigs added for a new total of 26,988 Compound primary key created for ctgPos2 table. Data reloaded.
2005-06-03 2005-02-22 Assembly bosTau1 problem with AGP file--truncated scaffolds agpFragValidate added to kent/src/hg/lib/agpFrag.c (please refer to makeBosTau1.doc)
2005-05-27 2004-10-04 sgpGene mm5 chrX missing reloaded tables
2005-03-22 2005-03-04 CCDS hg17 some records mis-mapped in PAR region (~30 ?) reported by user reloaded tables
2005-03-11 2005-02-14 8-way dm2 track built without droYak1 (reported by user) reloaded tables
2005-03-04 2004-09-13 Map Contigs mm5 non-C57BL contigs not filtered out (found by Heather and Daryl) reloaded table with just C57BL
2005-03-01 ensembl mm5 13 entries had chrMT instead of chrM and they had no protein sequence -- ensembl did not have them in their file (reported by user) reloaded table
2005-02-28 2004-07-23 stsMap hg17 change in filtering caused error in 0.1% of records. reported by user reloaded table
2004-12-15 miRNA hg17 change from collaborator
2004-10-19 contigs rn3 adjust to 0-based
2004-10-08 Perlegen and Haplotype hg16 8 coordinate corrections (see /cluster/data/qa/hg16/hapFix.sql) check add to checkTableCoords
2004-10-06 Conservation hg17, mm5, sacCer1 algorithm tweaks
2004-09-29 unk SGP Genes galGal2 data update
2004-09-27 BDGP Insertions dm1 small data corrections
2004-09-16 2004-08-21 Fly Proteins anoGam1, droYak1
2004-09-16 Human Proteins ci1, danRer1 data update, missing first exons
2004-09-16 2004-08-11 gnfAtlas2Distance hg17 completed run (previous run was truncated)
2004-09-16 2004-09-10 cytoband mm5 new data from NCBI
August 27, 2004 SNPs mm4 fix for bad alignments
August 23, 2004 Vega Genes hg16 new version of ldHgGene. 398 rows where 3' UTR extended.
August 20, 2004 2003 Rat/Mouse/Human (multiz) rn3 data update
August 19, 2004 March 19, 2004 STS Markers mm4 corrupted RH data; truncated alias column data and programs fixed by Yontau and Fan
August 13, 2004 July 26, 2004 Fish Clones hg17 2 rows with a missing element in bandEnds column data and programs fixed by Kate
August 13, 2004 April 15, 2004 Affy RAE230 Expression rn3 re-aligned when creating gene sorter. 223 rows deleted, 210 rows added. No changes to seq.
July 27, 2004 July 26, 2004 /gbdb/hg17/nib/chrN_random.nib (most, not all) hg17 missed June update extended hgwdev/hgwbeta script to include /gbdb (previously just tables)
July 20, 2004 Twinscan hg16 new version of ldHgGene (27 rows changed; exonCount + 1)
July 20, 2004 Ensembl hg16 new version of ldHgGene (37 rows changed; only 1 or 2 bases)
May 14, 2004 TFBS hg16, hg15 indices added
May 5, 2004 Geneid hg16, hg15, mm4, mm3, rn3, rn2 add stop codon
May 5, 2004 Twinscan hg16, hg15, mm3, rn3, rn2 add stop codon
May 3, 2004 Ensembl rn3 rebuild
April 20, 2004 dupSpMrna hg16 drop unused rows
April 16, 2004 Gene Sorter (Family Browser) *.knownToPfam remove duplicates
April 16, 2004 Gene Sorter (Family Browser) hg16 RT #951; atlas alignments
April 14, 2004 Human Dels panTro1 new data from Tarjei (2k out of 18k changed)
April 7, 2004 Geneid panTro1 fix errors in chr1
Mar 2, 2004 Map Contigs hg16 size updated for 5 random contigs
January 15, 2004 Assembly/Gap hg16 missed data update (chr4_random, chr8_random, chrX_random, chrUn_random)