Hi Bino, We don't have a method that will show everything you're interested in a single track, so you'll have to use multiple tracks.
You can use a bigWig track to display the graph. See this page for more info: http://genome.ucsc.edu/goldenPath/help/bigWig.html. You can process the numerical data down to itemRgb of bigBed items with a color code for the "height" of the data at that point. This is a color density graph. The item names can include the read count as part of the name. See this page for more info: http://genome.ucsc.edu/goldenPath/help/bigBed.html Turn on an appropriate gene track (which will have the strand arrows) to show the genes in these regions. 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 John, Bino wrote, On 01/21/11 14:33: > We are trying to provide users access to the data we have, via the ucsc > genome browser- which I think is the best thing to do because so may people > now use UCSC. The users come to our website and we process a small BedGraph > file that is sent to UCSC and it is then displayed to the user. The problem > is that the bedgraph format does not allow us to do what we want: we want to > plot something like a bar graph or a vertical line which has a height > proportional to a numeric we have (such as number of reads), we also want to > display the strand direction using some thing like the arrows that are > allowed for BED files but seem not allowed for BedGraph files. So my > questions are: > > 1. Is there any format or trick we can use to allow UCSC to display this > information simultaneously? > > 2. is there anyway to indicate the absolute numeric next to the bar graph? > Basically we want something that could look like this (anything similar would > be just fine - the vertical lines below represent the bar graph): > > | reads=20 > | | reads=10 > Gene p53 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< > > > 3. the description of several fields in the microarray track > http://genomewiki.ucsc.edu/index.php/Microarray_track (e.g., thickStart) are > missing, where can we get these info? Basically I am looking for the most > comprehensive bedfile > > Thanks > > Bino > > Asst. Professor > University of Pittsburgh School of Medicine 3080 Biomedical Science Tower 3 > 3501 Fifth Avenue, Pittsburgh, PA 15260,USA > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
