Hello again Bogdan, I realized I left out the 3'UTR part of your request. The method below stands but with the following modification (see comment within):
On 03/16/11 16:49, Pauline Fujita wrote: > Hello Bogdan, > > To get this data you will need to cross reference two of the tables from > our Gencode Genes track with the subset of items in our RepeatMasker > track that are tagged as Alu elements. You can do this using a couple > iterations of queries on our Table Browser > (http://genome.ucsc.edu/cgi-bin/hgTables) as follows: > > Round 1 (creating a custom track of Gencode items tagged as lincRNAs): > > group:Genes and Gene Prediction Tracks > track: Gencode Genes > table: wgEncodeGencodeAutoV4 > region: genome > > filter: click "create" > > then scroll down to the "Linked Tables" section and select the > 'wgEncodeGencodeClassesV4' table and click "Allow Filtering Using Fields > in Checked Tables" > > This should bring up a new section: > "hg19.wgEncodeGencodeClassesV4 based filters" > > In this section set: > transcriptType does match lincRNA > > Then click "submit". > > Now back in the main Table Browser menu select: > > output format: "custom track" > > Once you click on "get output" this will take you to a menu where you > can specify how to receive your custom track and you should pick "get > custom track in table browser". HERE: you should select: Create one BED record per: 3' UTR Exons (rather than the default of "Whole Gene") This should restrict your query to Alu elements in the RepeatMasker track that overlap with the 3'UTRs of the lincRNA items in the Gencode track. > > Round 2 (intersecting your custom track with Alu* elements in the > RepeatMasker track): > > Back in the table browser you should now select the following: > > group: Variation and Repeats > track: RepeatMasker > table: rmsk > region: genome > > filter: click "create" > > in the "Filter on Fields from hg19.rmsk" section set: > > repFamily does match Alu* > > and click "submit" > > Now back in the main Table Browser menu: > > intersection: click "create" > > and in the intersection menu select your custom track: > > group: Custom Tracks > track: (whatever you called the track from Round 1 - if you didn't > > change the default this will be something like > "ct_tbwgEncodeGencodeAutoV4") > table: this name will be similar > > then click submit and in the main menu select your output format of > choice and click "get output". > > Note that the lincRNAs in the Gencode track are predicted by Ensembl and > they may not therefore be experimentally verified. There are some other > ncRNA resources out there that you could try. http://www.ncrna.org is > one and from there, there is a link to fRNAdb which has ncRNA > annotations - they have an implementation of the Genome Browser. > > Best regards, > > Pauline Fujita > UCSC Genome Bioinformatics Group > http://genome.ucsc.edu > > > > On 03/02/11 13:30, Bogdan Tanasa wrote: >> Dear all, >> >> please could you let me know the way you recommend to identify >> mRNAs(lincRNAs) with ALU elements in 3' UTR ... thanks, >> >> >> Bogdan >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
