Hi Kavita, Unfortunately, there is no easy way to extract this information. The easiest way to get a sense of all the cell lines that had peaks in the relevant cluster regions is to view all of the peaks from the UW DNaseI HS ( http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeUwDnase) along with the Digital DNaseI Hypersensitivity Clusters track in the genome browser.
Hope this helps somewhat. If you have additional questions, please email the list. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Garg, Kavita <[email protected]> Date: Thu, May 31, 2012 at 10:23 AM Subject: Re: [Genome] Name of item in the table wgEncodeRegDnaseClustered To: Vanessa Kirkup Swing <[email protected]> Cc: [email protected] Vanessa, Thank you. Is there no way of getting information about cell types in a cluster from a table. kavita ----- Original Message ----- From: "Vanessa Kirkup Swing" <[email protected]> To: "Kavita Garg" <[email protected]> Cc: [email protected] Sent: Thursday, May 31, 2012 10:18:11 AM Subject: Re: [Genome] Name of item in the table wgEncodeRegDnaseClustered Hi Kavita, The name field represents the number of items in the cluster. To find out more information about each cluster, you can click on the item in the browser image and it will take you to a details page that will list all of the items in the cluster and the cell lines. Here is an example details page: http://genome.ucsc.edu/cgi-bin/hgc?db=hg19&c=chr21&o=33032260&t=33033430&g=wgEncodeRegDnaseClustered&i=58 There are 58 items in this cluster and you will see that the name is 58 when displayed in the browser. I hope this clarifies things for you. If you have further questions, please contact the list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Garg, Kavita <[email protected]> Date: Wed, May 30, 2012 at 5:10 PM Subject: [Genome] Name of item in the table wgEncodeRegDnaseClustered To: [email protected] Hi, In the table wgEncodeRegDnaseClustered representing Digital DNaseI Hypersensitivity Clusters from ENCODE, what is "name" ? And also, for each cluster, how do we determine the cell types. Here is the table schema: field example SQL type description bin 585 smallint(5) unsigned Indexing field to speed chromosome range queries. chrom chr1 varchar(255) Reference sequence chromosome or scaffold chromStart 10100 int(10) unsigned Start position in chromosome chromEnd 10330 int(10) unsigned End position in chromosome name 62 varchar(255) Name of item score 291 int(10) unsigned Score from 0-1000 thanks kavita _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
