Hi Kalyan, By CGIs do you mean CpG Islands? If so, we already have a track in the Genome Browser displaying these regions. To turn this track on from the main browser browser page, scroll down under the image to the "Regulation" track group and under CpG Islands click the drop-down menu and switch select full. For more information about the track, please click on the title "CpG Islands" above the drop-down to go to the track description page (http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=cpgIslandExt).
If instead you want to upload your own subset of CpG Islands, you can go to the Gateway page (http://genome.ucsc.edu/cgi-bin/hgGateway) and click on "add custom tracks." For detailed information about file formats accepted by our browser as custom tracks and step by step instructions on loading custom tracks, please see this page: http://genome.ucsc.edu/goldenPath/help/customTrack.html. By NXScore results are you referring to the Nucleosome Scores of the Nucleosome Exclusion Prediction data sets (hg18) accompanying the paper entitled "Prediction and analysis of nucleosome exclusion regions in the human genome" by Radwan A et al. from 2008? If so, from the genome.ucsc.edu page, you can click on the "Custom Tracks" link in the left-hand side bar. This will take you to the Custom Annotation Tracks page (http://genome.ucsc.edu/goldenPath/customTracks/custTracks.html) where the Nucleosome Exclusion Prediction data sets is listed as the fourth paragraph. You can see the scores of a particular chromosome by clicking on the chromosome number. I hope this information is helpful. Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Kalyan Ganguly wrote, On 02/11/11 16:11: > > Dear Colleague, > I followed the requirement of going through the archive before posting this > email. Failing to find an answer to my following questions I send this query > to > you. > > 1. How do I obtain a visual display of the CGIs within a given region of a > genome using Custom tracks option of UCSC Genome browser? CGI analysis sites > are > known to me. > > 2. How do I upload the NXScore results as a Custom Track on the UCSC Genome > Browser interface to obtain a figure on Nucleosome-exclusion regions of given > region of genomic DNA? > > > Thank you in anticipation of your step by step instructions. > Regards, > Kalyan > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
