Hi, We installed a local genome browser with minimal installation. I tried to load wig files to local database.
First, use wigEncode to make wig/wib files. l...@test01:~$ wigEncode PolII_eland_sorted2.wig PolII.wig PolII.wib Converted PolII_eland_sorted2.wig, upper limit 4385.00, lower limit 2.00 2. mkdir wib folder inside of /mnt/nfs/genomdata/gbdb/hg18/ 3. [l...@research ~]$ /opt/kent/hgLoadWiggle -pathPrefix=/mnt/nfs/genomdata/gbdb/hg18/wib hg18 wigExample PolII.wig Connected to database hg18 for track wigExample Creating wiggle table definition in hg18.wigExample Saving wiggle.tab WARNING: Exceeded chrM size 16624 > 16571. dropping 3 data point(s) Loading hg18 4. [l...@research ~]$ cp PolII.wib /mnt/nfs/genomdata/gbdb/hg18/wib/ 5. [l...@research trackDb]$ cd bin/kent/src/hg/makeDb/trackDb [l...@research trackDb]$ /opt/kent/hgTrackDb human hg18 trackDb_wigExample ../../lib/trackDb.sql . .... .... Loaded 4374 track descriptions total Loaded database hg18 6. [l...@research trackDb]$ /opt/kent/hgFindSpec human hg18 hgFindspec_wigExample ../../lib/hgFindSpec.sql . found include file: ./human/hg18/trackDb.chainNet.ra found include file: ./human/hg18/trackDb.encode.ra found include file: ./human/hg18/trackDb.encodeGenes.ra found include file: ./human/hg18/trackDb.encodeTxLevels.ra found include file: ./human/hg18/trackDb.encodeChip.ra found include file: ./human/hg18/trackDb.encodeChrom.ra found include file: ./human/hg18/trackDb.encodeCompAndVar.ra found include file: ./human/hg18/trackDb.wgEncode.ra found include file: ./human/hg18/wgEncodeRikenCage.alpha.ra found include file: ./human/hg18/wgEncodeRikenCage.beta.ra found include file: ./human/hg18/wgEncodeCaltechRnaSeq.alpha.ra found include file: ./human/hg18/wgEncodeCaltechRnaSeq.beta.ra found include file: ./human/hg18/wgEncodeGisPet.alpha.ra found include file: ./human/trackDb.encode.ra found include file: ./human/trackDb.chainNet.ra found include file: ./trackDb.chainNet.ra Loaded 216 search specs total Loaded database hg18 7. [l...@research trackDb]$ locate hg.conf /var/www/html/genomebrowser/cgi-bin/hg.conf vim /var/www/html/genomebrowser/cgi-bin/hg.conf change db.trackDb to db.trackDb=trackDb_wigExample,trackDb Now, I open local genome browser, still can't see my wigExample file. mysql> show tables; | wigExample | | xenoEst | | xenoMrna | | xenoRefFlat | | xenoRefGene | | xenoRefSeqAli | | yaleBertoneTars | +------------------------------------------------------------------+ mysql> select tableName from trackDb; | wgEncodeYaleChIPseqViewPeaks | | wgEncodeYaleChIPseqViewSignal | | wgRna | | xenoEst | | xenoMrna | | xenoRefGene | | yaleBertoneTars | +------------------------------------------------------------------+ Any help appreciate!!! On Wed, May 5, 2010 at 4:30 PM, Jennifer Jackson <[email protected]> wrote: > Hello Tiandao, > > Just to double check, you followed the procedures in this doc to load your > data? If so, there should be a trackDb entry. > > src/product/README.trackDb > > Just loading the table will not "add" it to a database. You have to follow > the instructions in the readme. Please try again using the README as a guide > and see if that works, > > > Thanks, > Jennifer > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > On 5/5/10 2:20 PM, Tiandao Li wrote: > >> I created pol2 as genome last night, however, I loaded it to hg18 today, >> mysql> use hg18; >> >> mysql> select * from trackDb; >> ..... >> 2671 rows in set (0.02 sec) >> >> I found wigExample by :mysql> show tables; >> but not mysql> select tableName from trackDb; >> >> >> >> On Wed, May 5, 2010 at 4:05 PM, Jennifer Jackson <[email protected] >> <mailto:[email protected]>> wrote: >> >> Hello - >> >> The track should appear under whatever track group you assigned it >> to in the trackDb.ra file. It will appear in the Table browser also >> under this track group. The table _is_ the file unless you export it >> again using the Table browser. >> >> If are are using pol2 as "genome", then type in mySQL: >> >> % use pol2; >> % select * from trackDb; >> (your track should show up, telling you what grp it was assigned to) >> >> If you are using hg18 as Hiram suggest, then type in the same things >> in mySQL: >> % use hg18 >> % select * from trackDb; >> (you can add a "where" clause to limit output if you want) >> >> If this does not help, please let us know, >> >> Jennifer >> >> --------------------------------- >> Jennifer Jackson >> UCSC Genome Informatics Group >> http://genome.ucsc.edu/ >> >> On 5/5/10 1:19 PM, Tiandao Li wrote: >> >> Hi Jennifer, >> >> Looks like I load wig file to mysql database, however, how could >> I see >> it on local genome browser? I refresh the webpage, can't find >> where can >> I find wigExample table or my wig file? >> >> >> >> On Wed, May 5, 2010 at 3:08 PM, Jennifer Jackson >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> wrote: >> >> Hi Tiandao, >> >> I am glad you followed Hiram's advice and were able to load >> your >> data in hg18. However, I am not sure what your new question >> is about: >> >> >> > I refresh our local browser, where can I find the wig file? >> > >> > Thanks!! >> >> Would you be able to clarify? >> >> Thanks, >> Jennifer >> >> >> --------------------------------- >> Jennifer Jackson >> UCSC Genome Informatics Group >> http://genome.ucsc.edu/ >> >> On 5/5/10 12:38 PM, Tiandao Li wrote: >> >> Hello, >> >> [l...@research ~]$ /opt/kent/hgLoadWiggle hg18 wigExample >> PolII.wigConnected to database hg18 for track wigExample >> Creating wiggle table definition in hg18.wigExample >> Saving wiggle.tab >> WARNING: Exceeded chrM size 16624 > 16571. dropping 3 >> data point(s) >> Loading hg18 >> >> >> Looks like I upload wig files. >> >> mysql> show columns from wigExample; >> >> >> +------------+----------------------+------+-----+---------+-------+ >> | Field | Type | Null | Key | >> Default | Extra | >> >> >> +------------+----------------------+------+-----+---------+-------+ >> | bin | smallint(5) unsigned | NO | | NULL >> | | >> | chrom | varchar(255) | NO | MUL | NULL >> | | >> | chromStart | int(10) unsigned | NO | | NULL >> | | >> | chromEnd | int(10) unsigned | NO | | NULL >> | | >> | name | varchar(255) | NO | | NULL >> | | >> | span | int(10) unsigned | NO | | NULL >> | | >> | count | int(10) unsigned | NO | | NULL >> | | >> | offset | int(10) unsigned | NO | | NULL >> | | >> | file | varchar(255) | NO | | NULL >> | | >> | lowerLimit | double | NO | | NULL >> | | >> | dataRange | double | NO | | NULL >> | | >> | validCount | int(10) unsigned | NO | | NULL >> | | >> | sumData | double | NO | | NULL >> | | >> | sumSquares | double | NO | | NULL >> | | >> >> >> +------------+----------------------+------+-----+---------+-------+ >> 14 rows in set (0.00 sec) >> >> I refresh our local browser, where can I find the wig file? >> >> Thanks!! >> >> >> On Wed, May 5, 2010 at 2:30 PM, Tiandao Li >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>>> wrote: >> >> Hi Jen, >> >> mysql> show databases; >> +--------------------+ >> | Database | >> +--------------------+ >> | information_schema | >> | hg18 | >> | hgFixed | >> | hgcentral | >> | mysql | >> | pol2 | >> | proteins040115 | >> | proteins040315 | >> | proteins040515 | >> | proteins050415 | >> | proteins051015 | >> | proteins060115 | >> | proteins070202 | >> | proteins080707 | >> | proteins090821 | >> | proteome | >> | sp040115 | >> | sp040315 | >> | sp040515 | >> | sp051015 | >> | sp060115 | >> | sp070202 | >> | test | >> | uniProt | >> +--------------------+ >> 24 rows in set (0.00 sec) >> >> mysql> select * from grp; >> >> >> >> >> +------------------+-------------------------------------------------+----------+-----------------+ >> | name | label >> | priority | defaultIsClosed | >> >> >> >> >> +------------------+-------------------------------------------------+----------+-----------------+ >> | user | Custom Tracks >> | 1 | 0 | >> | map | Mapping and Sequencing Tracks >> | 2 | 0 | >> | genes | Genes and Gene Prediction Tracks >> | 3 | 0 | >> | rna | mRNA and EST Tracks >> | 4 | 0 | >> | regulation | Regulation >> | 5 | 1 | >> | compGeno | Comparative Genomics >> | 6 | 0 | >> | varRep | Variation and Repeats >> | 7 | 0 | >> | encodeGenes | Pilot ENCODE Regions and Genes >> | 8.1 | 1 | >> | encodeTxLevels | Pilot ENCODE Transcription >> | 8.2 | 1 | >> | encodeChip | Pilot ENCODE Chromatin >> Immunoprecipitation >> | 8.3 | 1 | >> | encodeChrom | Pilot ENCODE Chromatin Structure >> | 8.4 | 1 | >> | encodeCompAndVar | Pilot ENCODE Comparative >> Genomics and >> Variation >> | 8.5 | 1 | >> | encodeAnalysis | Pilot ENCODE Analysis >> | 8.9 | 1 | >> | phenDis | Phenotype and Disease Associations >> | 2.5 | 1 | >> | expression | Expression >> | 4.5 | 1 | >> >> >> >> >> +------------------+-------------------------------------------------+----------+-----------------+ >> 15 rows in set (0.00 sec) >> >> mysql> select * from chromInfo; >> >> +---------------+-----------+----------------------------------+ >> | chrom | size | fileName >> | >> >> +---------------+-----------+----------------------------------+ >> | chr1 | 247249719 | >> /gbdb/hg18/nib/chr1.nib | >> | chr1_random | 1663265 | >> /gbdb/hg18/nib/chr1_random.nib | >> | chr10 | 135374737 | >> /gbdb/hg18/nib/chr10.nib | >> | chr10_random | 113275 | >> /gbdb/hg18/nib/chr10_random.nib | >> | chr11 | 134452384 | >> /gbdb/hg18/nib/chr11.nib | >> | chr11_random | 215294 | >> /gbdb/hg18/nib/chr11_random.nib | >> | chr12 | 132349534 | >> /gbdb/hg18/nib/chr12.nib | >> | chr13 | 114142980 | >> /gbdb/hg18/nib/chr13.nib | >> | chr13_random | 186858 | >> /gbdb/hg18/nib/chr13_random.nib | >> | chr14 | 106368585 | >> /gbdb/hg18/nib/chr14.nib | >> | chr15 | 100338915 | >> /gbdb/hg18/nib/chr15.nib | >> | chr15_random | 784346 | >> /gbdb/hg18/nib/chr15_random.nib | >> | chr16 | 88827254 | >> /gbdb/hg18/nib/chr16.nib | >> | chr16_random | 105485 | >> /gbdb/hg18/nib/chr16_random.nib | >> | chr17 | 78774742 | >> /gbdb/hg18/nib/chr17.nib | >> | chr17_random | 2617613 | >> /gbdb/hg18/nib/chr17_random.nib | >> | chr18 | 76117153 | >> /gbdb/hg18/nib/chr18.nib | >> | chr18_random | 4262 | >> /gbdb/hg18/nib/chr18_random.nib | >> | chr19 | 63811651 | >> /gbdb/hg18/nib/chr19.nib | >> | chr19_random | 301858 | >> /gbdb/hg18/nib/chr19_random.nib | >> | chr2 | 242951149 | >> /gbdb/hg18/nib/chr2.nib | >> | chr2_random | 185571 | >> /gbdb/hg18/nib/chr2_random.nib | >> | chr20 | 62435964 | >> /gbdb/hg18/nib/chr20.nib | >> | chr21 | 46944323 | >> /gbdb/hg18/nib/chr21.nib | >> | chr21_random | 1679693 | >> /gbdb/hg18/nib/chr21_random.nib | >> | chr22 | 49691432 | >> /gbdb/hg18/nib/chr22.nib | >> | chr22_random | 257318 | >> /gbdb/hg18/nib/chr22_random.nib | >> | chr22_h2_hap1 | 63661 | >> /gbdb/hg18/nib/chr22_h2_hap1.nib | >> | chr3 | 199501827 | >> /gbdb/hg18/nib/chr3.nib | >> | chr3_random | 749256 | >> /gbdb/hg18/nib/chr3_random.nib | >> | chr4 | 191273063 | >> /gbdb/hg18/nib/chr4.nib | >> | chr4_random | 842648 | >> /gbdb/hg18/nib/chr4_random.nib | >> | chr5 | 180857866 | >> /gbdb/hg18/nib/chr5.nib | >> | chr5_random | 143687 | >> /gbdb/hg18/nib/chr5_random.nib | >> | chr5_h2_hap1 | 1794870 | >> /gbdb/hg18/nib/chr5_h2_hap1.nib | >> | chr6 | 170899992 | >> /gbdb/hg18/nib/chr6.nib | >> | chr6_random | 1875562 | >> /gbdb/hg18/nib/chr6_random.nib | >> | chr6_cox_hap1 | 4731698 | >> /gbdb/hg18/nib/chr6_cox_hap1.nib | >> | chr6_qbl_hap2 | 4565931 | >> /gbdb/hg18/nib/chr6_qbl_hap2.nib | >> | chr7 | 158821424 | >> /gbdb/hg18/nib/chr7.nib | >> | chr7_random | 549659 | >> /gbdb/hg18/nib/chr7_random.nib | >> | chr8 | 146274826 | >> /gbdb/hg18/nib/chr8.nib | >> | chr8_random | 943810 | >> /gbdb/hg18/nib/chr8_random.nib | >> | chr9 | 140273252 | >> /gbdb/hg18/nib/chr9.nib | >> | chr9_random | 1146434 | >> /gbdb/hg18/nib/chr9_random.nib | >> | chrM | 16571 | >> /gbdb/hg18/nib/chrM.nib | >> | chrX | 154913754 | >> /gbdb/hg18/nib/chrX.nib | >> | chrX_random | 1719168 | >> /gbdb/hg18/nib/chrX_random.nib | >> | chrY | 57772954 | >> /gbdb/hg18/nib/chrY.nib | >> >> +---------------+-----------+----------------------------------+ >> 49 rows in set (0.00 sec) >> >> >> mysql> select * from trackDb; >> >> .... >> 2671 rows in set (0.02 sec) >> >> >> mysql> select * from hgFindSpec; >> .... >> 142 rows in set (0.00 sec) >> >> >> mysql> select * from gold; >> ERROR 1146 (42S02): Table 'hg18.gold' doesn't exist >> mysql> select * from gap; >> ERROR 1146 (42S02): Table 'hg18.gap' doesn't exist >> >> However no gap and gold tables. The question is I >> don't know >> how to >> load wig files to mysql. >> >> I created person db, pol2, so I can upload my wig >> files to >> there, >> looks like I need to load them to hg18, right? >> >> Thanks! >> >> >> On Wed, May 5, 2010 at 1:32 PM, Jennifer Jackson >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>>> wrote: >> >> Hello Tiandao, >> >> The six required tables need to be added to your >> pol2 >> database. >> >> >> http://genomewiki.cse.ucsc.edu/index.php/Minimal_Browser_Installation >> >> A minimal browser database [aka assembly] needs >> six tables: >> grp >> chromInfo >> trackDb >> hgFindSpec >> gold >> gap >> >> Try this and let us know if it does not solve >> the problem, >> >> Thanks >> jen >> >> >> --------------------------------- >> Jennifer Jackson >> UCSC Genome Informatics Group >> http://genome.ucsc.edu/ >> >> On 5/5/10 11:18 AM, Tiandao Li wrote: >> >> Hi, >> >> We installed a minimal genome browser >> locally with hg18 >> only. We want to >> load generated wig files (human hg18) so we >> can view >> them on >> local browser. >> We used wigEncode to generate wig and wib >> files. >> >> peak$ wigEncode PolII_eland_sorted2.wig >> PolII.wig >> PolII.wib >> Converted PolII_eland_sorted2.wig, upper >> limit 4385.00, >> lower limit 2.00 >> >> then >> mysql> create database pol2; >> >> copy system-wide hg.conf to my folder as >> .hg.conf >> >> ~]$ /opt/kent/hgLoadWiggle pol2 xxx PolII.wig >> >> Can't start query: >> select * from chromInfo >> >> mySQL error 1146: Table 'pol2.chromInfo' >> doesn't exist >> >> Please show me how to load wig files to >> local mysql >> database. >> >> Thanks!!! >> _______________________________________________ >> Genome maillist - [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] <mailto: >> [email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>> >> >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> >> >> >> >> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
