Hi Rocky, It sounds like the "ENCODE RNA Binding Proteins Tracks" on hg19 ( http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr21&g=wgEncodeRbpSuper)maybe of interest to you. You will need to decide what tracks and subtracks interest you. Please read the description pages for each track to determine which of the subtracks maybe of interest of you.
To determine the table that is associated with a subtrack you can click on the schema links listed next to the subtracks. For example, if you go to the "SUNY RIP GeneST Track" description page ( http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr21&g=wgEncodeSunyAlbanyGeneSt) which is a track listed in "ENCODE RNA Binding Proteins Tracks" you will see a list of subtracks which have a blue "schema" link which will tell you the table that is being used. The schema link will also tell you the type of data that is stored in the table. For example the table for the "GM12878 CELF1 RBP Associated RNA by RIP-chip GeneST from ENCODE/SUNY" subtrack is "wgEncodeSunyAlbanyGeneStGm12878Celf1RbpAssocRnaV2". If you were using the table browser, the table you would select would be wgEncodeSunyAlbanyGeneStGm12878Celf1RbpAssocRnaV2. If you were using this link: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ you will have two options: wgEncodeSunyAlbanyGeneStGm12878Celf1RbpAssocRnaV2.sql 09-Oct-2011 19:28 1.8K wgEncodeSunyAlbanyGeneStGm12878Celf1RbpAssocRnaV2.txt.gz 09-Oct-2011 19:28 15K Notice that the the table name is part of the file name. If you aren't familiar with the table browser, please see Table Browser User's Guide* * (http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html). If you have further questions, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: 하오잠 로 <[email protected]> Date: 2011/10/27 Subject: [Genome] [Rocky] - genomic coordinates for RNA binding proteins To: [email protected] UCSC Genome Browser Team Hello Sir/Miss, I would like to retrieve list of RNA binding proteins or domain with their genomic positions [i.e. chromosomal coordinates] from UCSC genome browser. I have located an ftp site with refFlat.txt http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ and another option using regulations from UCSC table browser. Could you please tell me which one should like click for extracting what I am looking for. I would be glad for your assistance. With regards, Rocky Haojam Seoul National University _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
