Dear Brooke, Thanks! I have two more questions. 1.Why the number of simple repeats downloaded from the simpleRepeat table is different with it in rmsk table in the rep_class Simple_repeat? 2.There are so many tables for H3K4me3, so if I want to map this histone modification in prostate cancer, which table is the best choice? Thanks in advance!
Best, Lei -----Original Message----- From: Brooke Rhead [mailto:[email protected]] Sent: Friday, October 07, 2011 10:52 PM To: Gu, Lei Cc: [email protected] Subject: Re: [Genome] extract SINE/LINE/ALU information Hi Lei, You can use the Table Browser (the "Tables" link at the top of the page) to get data in BED format. Select the clade, genome, and assembly you are interested in, then: group: variation and repeats track: RepeatMasker table: rmsk output format: BED - browser extensible data This should get you the contents of the RepeatMasker track in BED format. You can also filter your output, or limit your output to certain regions. For more information, see: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28 If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 10/7/11 5:54 AM, Gu, Lei wrote: > HI, I want to extract the SINE/LINE/ALU information in BED format > fromhuman genome. Would you please tell me how to do that? > Thanks! > Lei > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
