Hello again, As we have both experienced, this particular query creates too much data for the Table Browser to sort through for certain assemblies. This is true for human but not true for some of the smaller assemblies (such as dog).
The only alternate solution worked out is to perform a direct mySQL query. Use our public mySQL server client to do this: http://genome.ucsc.edu/FAQ/FAQdownloads#download29 Below are links, sample queries and other help to get your started. Good luck with your research and thank you for your patience while we worked through this, Jennifer Jackson UCSC Genome Bioinformatics Group ------------------------------------- Sample query for obtaining all spliced ESTs for a chromosome. The data for intronEst in the latest human assembly (that represents the Spliced ESTs track) is a divided table, one per chrom, in the human database. This is not true for all DBs or tracks. mysql -h genome-mysql.cse.ucsc.edu -u genome hg18 -Be 'select * from chr10_intronEst,gbCdnaInfo,tissue where gbCdnaInfo.acc = chr10_intronEst.qName and tissue.id = gbCdnaInfo.tissue and tissue.name like "%brain%";' To limit by a particular region on the chrom, add something like this into the "where" clause: and tEnd ("<" or ">") some_genomic_coordinate and tStart ("<" or ">") some_genomic_coordinate Sample query for the mRNA track limited to a region of genomic: mysql -h genome-mysql.cse.ucsc.edu -u genome hg18 -Be 'select tName,tStart,tEnd,qName,name from all_mrna,gbCdnaInfo,tissue where tName = "chr3" and tEnd > 37009983 and tStart < 37067341 and gbCdnaInfo.acc = qName and tissue.id = gbCdnaInfo.tissue and tissue.name like "%brain%";' mySQL language help (not from UCSC, we do not endorse 3rd party software/tools, but this is a great reference for syntax help) http://dev.mysql.com/doc/refman/5.1/en/ Check out the Section Navigation section on the left of the page List of all tables from the Spliced EST track in the latest human (hg18) datbase: mysql> show tables like '%intron%'; +---------------------------+ | Tables_in_hg18 (%intron%) | +---------------------------+ | chr10_intronEst | | chr10_random_intronEst | | chr11_intronEst | | chr11_random_intronEst | | chr12_intronEst | | chr13_intronEst | | chr13_random_intronEst | | chr14_intronEst | | chr15_intronEst | | chr15_random_intronEst | | chr16_intronEst | | chr16_random_intronEst | | chr17_intronEst | | chr17_random_intronEst | | chr18_intronEst | | chr18_random_intronEst | | chr19_intronEst | | chr19_random_intronEst | | chr1_intronEst | | chr1_random_intronEst | | chr20_intronEst | | chr21_intronEst | | chr21_random_intronEst | | chr22_h2_hap1_intronEst | | chr22_intronEst | | chr22_random_intronEst | | chr2_intronEst | | chr2_random_intronEst | | chr3_intronEst | | chr3_random_intronEst | | chr4_intronEst | | chr4_random_intronEst | | chr5_h2_hap1_intronEst | | chr5_intronEst | | chr5_random_intronEst | | chr6_cox_hap1_intronEst | | chr6_intronEst | | chr6_qbl_hap2_intronEst | | chr6_random_intronEst | | chr7_intronEst | | chr7_random_intronEst | | chr8_intronEst | | chr8_random_intronEst | | chr9_intronEst | | chr9_random_intronEst | | chrM_intronEst | | chrX_intronEst | | chrX_random_intronEst | | chrY_intronEst | +---------------------------+ 49 rows in set (0.08 sec) Vorstman, J.A.S. wrote: > Hi there, > > Does anyone know how to obtain, using the UCSC table browser, Human spliced ESTs, but only those that are expressed in the brain? I just can't figure it out; in the genome browser I can select to include tissue = brain which seems to work fine. Unfortunately, in the table browser I can't find this selection option. Perhaps somebody knows the solution to this problem? Many thanks, Jacob > > J.A.S. Vorstman, MD PhD > > > University Medical Centre Utrecht > Dept of Psychiatry, A00.241 > Heidelberglaan 100, 3584CX > The Netherlands > Phone ( ) 31 88 755 8180 > Fax ( ) 31 88 755 5406 > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
