Hi Lei, 1. These are two different programs and use two different measurements. Read the description page for each. I think that will answer your questions: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=rmsk <http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=rmsk> http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=simpleRepeat <http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=simpleRepeat>
2. First, take a look at the ENCODE Cell Lines page: http://genome.ucsc.edu/ENCODE/cellTypes.html You can search that page prostate cell lines (just use your browsers "find" function in the page). I believe there are a few. Then go to Track Search (http://genome.ucsc.edu/cgi-bin/hgTracks, click on the Track Search button!). Click on the Advanced tab. For "Cell, tissure, DNA sample" enter one of the cell lines you found on the ENCODE Cell Lines page. Then for Antibody or Target Protein, select both H3K4me3 and H3K4me3B, and then click search. That should narrow down the list of table to ones relavent to you area of research. Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 10/10/11 6:21 AM, Gu, Lei wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
