Hello, Gordon. One of our engineers mentioned that whether or not a table has a range/values link is, among other things, a function of table size. The RepeatMasker table for hg19 is about 13 times larger than the same table in hg18 which explains the absence of the range/value links in hg19.
Probably the easiest way to obtain the information you're looking for is to perform a query on the public MySQL server. In your particular case, you would want to run the following queries: select distinct repClass from rmsk; select distinct repFamily from rmsk; The output is as follows: mysql> use hg19 Database changed mysql> select distinct repClass from rmsk; +----------------+ | repClass | +----------------+ | Simple_repeat | | Satellite | | LINE | | DNA | | SINE | | LTR | | Low_complexity | | Unknown | | snRNA | | tRNA | | DNA? | | srpRNA | | rRNA | | RC | | Other | | SINE? | | scRNA | | RNA | | LTR? | | Unknown? | | LINE? | +----------------+ 21 rows in set (3.95 sec) mysql> select distinct repFamily from rmsk; +----------------+ | repFamily | +----------------+ | Simple_repeat | | telo | | L1 | | hAT-Charlie | | MIR | | L2 | | CR1 | | ERVL-MaLR | | Alu | | hAT | | ERVL | | LTR | | Low_complexity | | ERV1 | | hAT-Tip100 | | TcMar-Tigger | | ERVL? | | RTE | | Unknown | | ERVK | | snRNA | | MuDR | | tRNA | | DNA? | | hAT-Blackjack | | Satellite | | srpRNA | | TcMar | | rRNA | | Gypsy | | TcMar-Tc2 | | RTE-BovB | | PiggyBac | | DNA | | TcMar? | | TcMar-Mariner | | Helitron | | Gypsy? | | hAT? | | SINE | | Other | | L1? | | Dong-R4 | | SINE? | | scRNA | | Deu | | RNA | | PiggyBac? | | centr | | Helitron? | | ERV | | LTR? | | Merlin | | Unknown? | | Penelope? | | acro | +----------------+ 56 rows in set (3.65 sec) In the future, please know that this option is available to you and that you can easily adjust it depending on your needs. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Assaf Gordon Sent: Tuesday, November 29, 2011 11:40 AM To: [email protected] Subject: [Genome] missing "range/values" buttons in some tables in Table Browser ? Hello, In the Table Browser, while viewing a "table schema", there used to be links to show all possible values. It seems that in some tables in the current version of genome browser, these links are missing - or perhaps I'm doing something wrong ? Compare: hg19 Human mRNA table - it has the "range/values" link in the "info" column: === http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=rna&hgta_track=mr na&hgta_table=all_mrna&hgta_doSchema=describe+table+schema === with: hg19 Repeat Masker table - no "info" column: === http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=varRep&hgta_track =rmsk&hgta_table=rmsk&hgta_doSchema=describe+table+schema === I'm asking because clicking on the "values" link was a quick way to find out all possible values for the "repClass" and "repFamily" in the Repeat Masker table, to be later used with the "filter" option in the Table Browser. Thanks, -gordon _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
