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, mm8,mm7,mm6,mm5, rn4,rn3,danRer4, danRer3,danRer2,danRer1, bosTau2,xenTro2,xenTro1 |
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, 2005-06-03 |
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) |