Hi Rajendra, Since you are a new user, I recommend these open helix tutorials which can be found here:
http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml 1) I am assuming that you are referring to these tracks on the hg19 assembly: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr7&g=wgEncodeTfBindingSuper There are 4 transcription factor tracks. If you click on one of the 4 blue links, this will take you to a track description page with more information about the data in the track. Here is a more advanced tutorial to help you understand how to look at this type of data: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=116 2) If you are looking for a specific type track, I recommend using our track search feature: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hgt_tSearch=1&tsCurTab=advancedTab Here is a list of antibodies that you may use to narrow down your search: http://genome.ucsc.edu/ENCODE/antibodies.html 3) To find out more about the a specific track, click on the blue link in the browser where it says "Conservation". Here is the direct link to the conservation track on the hg19 assembly: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chrX&g=cons46way Scroll down to the description section to find out the details about the track. To extract specific data from any of our tracks, use the table browser tool which you can get to by clicking on "Tables" from the blue navigation bar. Here is a tutorial to help you with the table browser: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28 I hope this helps. If you have further questions, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Rajendra kumar chauhan <[email protected]> Date: Thu, Aug 25, 2011 at 6:35 AM Subject: [Genome] Regarding TFBS from Chip Seq data To: [email protected] Hi, I am confused about some of the tracks of UCSC browser. 1.) I would like to know about the transcription factor binding site track data taken from the Transfac,Where do I find it..? 2.) I want to use the Chip seq data for TFBS,But I am not pretty sure about the general track,which I can use,As I am looking for the data from Ubiquitously associated Transcription factor binding site pull down using some antibodies. 3.) Can you please tell me something more about the Conservation track,Actually how to do that,I am looking for some constrained sequences,I want to give a condition for conserved sequences,Which are lets say atleast 100 bp long and have 70 % identity. I shall be thankful to you. I am a new user,So expecting a timely guidance -- *"with best regards" Rajendra Kumar Chauhan **Department of Genetics Univerity of Groningen (RUG) The Netherlands * *Mobile:- +31-686185912* _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
