Hi Shan, You might also be interested in our new tool, Genome Graphs. It is the 7th item down on the blue link bar on the left of our home page (genome.ucsc.edu), or you can reach it directly as
http://genome.ucsc.edu/cgi-bin/hgGenome It displays all chromosomes in a single view. You can upload your data using a very simple format -- click on the upload button for more info. Hope that helps, Angie On Mon, 20 Jul 2009, Jennifer Jackson wrote: > Hello Shan, > > One idea is to use a series of Custom tracks to provide some data > visualization. How to tackle NextGen sequencing & multiple genomes is an > important tool development topic for us, but for now, our recommendation is > as follows: > > Basic plan: > 1) select which chromosome to use as your "base". > 2) run the sequence(s) as a BLAT against entire genome. Note the chromosome + > coordinates that are not in your base chromosome. Save the results against > the base chromosome as a custom track. > 3) extract sequence (get DNA, Table browser) from other non-base chromosomes. > BLAT this portion of non-base genomic against the entire genomic. Save > results against the base chromosome as custom track. > 4) open the browser window at the base location. There should be a series of > custom tracks in the top group - the query sequence(s) and all non-base > chromosomes. > > Options: > A) the sequences will not be "aligned" to the non-base chromosomes. > Therefore, you may want to do this a few times, once for each genomic > location (one than one "base"). > B) instead of running a BLAT to align one chromosome to another, use the Self > Chain track. > C) expand BLAT alignment to not only include the component short reads but > the transcript itself (if not in a track already or if modified from the > public version). > D) open tracks such as Repeat Masker, Self Chain, UCSC/RefSeq genes, > Conservation, and maybe also some EST/mRNA tracks for context. > E) save the results in a Session to keep them around longer and to share with > others (be sure to keep backups). > > Help Links: > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Sessions > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks > http://genome.ucsc.edu/cgi-bin/hgLiftOver > > If a better method comes up in the next few days, we will send an update. > > Thank you, > Jennifer Jackson > > ----- Original Message ----- > From: "Shan Yang" <[email protected]> > To: [email protected] > Sent: Monday, July 20, 2009 11:48:37 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Showing data on different chromosomes > > > Hi, > > I have some next generation sequencing data (NGS) that detect > chimeric fusion transcripts. Basically, a pair of reads will cover > two regions that are on different chromosomes. The current genome > browser only allows viewing one chromosome at a time. I am wondering > if you have any tool that can show that kind of data where I can > view multiple chromosomes in one screen. > > Thank you very much! > > Shan > > > > > _______________________________________________ > 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
