Hello again Yu, I'm sorry for any misunderstanding. bedGraphs cannot handle overlapping data, and will behave in unexpected ways if given any. This means that your positive and negative strand data cannot be displayed together if they have overlapping regions.
Unfortunately, given your current needs, I think it would be best that you use two separate custom tracks to represent your data. You will lose the overlap, but will be able to customize the color and display of each track to your liking. We are working on a means to overlay separate data sets, but we currently have no time line as to when this feature will be added. Best Antonio Coelho UCSC Genome Bioinformatics Group Yuan Jian wrote: > thanks. > several questions for the "negative bar" > 1/ how to change the color for "negative bar"? > 2/ how to set yLineMark for negative bar? > 2/ when I gave positive and negative value for the same region with > two lines, only one is shown. when I gave pos and neg to the regions > with the same start locus and different end locus, both went to the > negative bar. I am not very clear the logical. could you please tell > me more details for the negative bar? > > Anji > > thanks > > > --- On *Fri, 4/6/10, Antonio Coelho /<anto...@soe.ucsc.edu>/* wrote: > > > From: Antonio Coelho <anto...@soe.ucsc.edu> > Subject: Re: [Genome] custom track with variable span > To: "Yuan Jian" <jayuan2...@yahoo.com> > Cc: gen...@soe.ucsc.edu > Received: Friday, 4 June, 2010, 11:17 PM > > Hello Yu, > It is possible to display bars below the line by giving them > negative > values. You could try making all of your negative strand values be > negative, which would separate them from your positive strands. > However, any overlapping entries will not display properly. > Unfortunately, there is no way of avoiding that, so you may have more > luck using two separate displays. > > Sorry for the inconvenience, and best of luck. Please contact us > again if you have other questions. > Best > Antonio Coelho > UCSC Genome Bioinformatics Group > > Yuan Jian wrote: > > Now I can use bedGraph to show bar for variable regions. my > another question is > > I want to show two bars on two sides of the region to show + and > - strand. > > one bar is up of a line (as normal), another bar is on opposite > side. > > > > __ > > | | > > something like ------------------------------------------- > > | | > > > > | | > > > > ---- > > > > > > thanks > > YU > > > > can I show the bar in up and down of the line > > > > --- On Wed, 2/6/10, Jennifer Jackson <j...@soe.ucsc.edu > </mc/compose?to=...@soe.ucsc.edu>> wrote: > > > > From: Jennifer Jackson <j...@soe.ucsc.edu > </mc/compose?to=...@soe.ucsc.edu>> > > Subject: Re: [Genome] custom track with variable span > > To: "Yuan Jian" <jayuan2...@yahoo.com > </mc/compose?to=jayuan2...@yahoo.com>> > > Cc: gen...@soe.ucsc.edu </mc/compose?to=gen...@soe.ucsc.edu> > > Received: Wednesday, 2 June, 2010, 6:16 PM > > > > Hello, > > > > Using the bedGraph format would allow you to specify different > spans in a single graphing custom track file. > > > > http://genome.ucsc.edu/goldenPath/help/bedgraph.html > > > > Data format: > > Following the track definition line are the track data > > in four column BED format. > > > > chromA chromStartA chromEndA dataValueA > > chromB chromStartB chromEndB dataValueB > > > > If the dataset is large, once you have the data in bedGraph > format, convert to bigWig. > > > > http://genome.ucsc.edu/goldenPath/help/bigWig.html > > (see "Example Three") > > > > General graphing track help: > > > > http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format > > > > Hopefully this addresses your question, but please let us know > if you need more assistance or if your question has been > misunderstood. > > > > Thanks, > > Jennifer > > > > --------------------------------- > > Jennifer Jackson > > UCSC Genome Informatics Group > > http://genome.ucsc.edu/ > > > > On 6/1/10 12:19 AM, Yuan Jian wrote: > > > >> Dear UCSC genome team, > >> > >> variableStep in wiggle custom track format, how can I change > span width for different item as below? > >> > >> browser position chr19:59304200-59310700 > >> track type=wiggle_0 name="variableStep" > description="variableStep format" \ > >> visibility=full autoScale=off viewLimits=0.0:25.0 > color=50,150,255 \ > >> yLineMark=11.76 yLineOnOff=on priority=10 > >> variableStep chrom=chr19 > >> 59304701 span=100 10.0 > >> 59304901 span=200 12.5 > >> 59305401 span=300 15.0 > >> 59305601 span=100 17.5 > >> 59305901 span=100 20.0 > >> 59306081 span=100 17.5 > >> 59306301 span=300 15.0 > >> 59306691 span=300 12.5 > >> 59307871 span=100 10.0 > >> > >> > >> > >> > >> > >> _______________________________________________ > >> Genome maillist - Genome@lists.soe.ucsc.edu > </mc/compose?to=gen...@lists.soe.ucsc.edu> > >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > >> > > > > > > > > > > _______________________________________________ > > Genome maillist - Genome@lists.soe.ucsc.edu > </mc/compose?to=gen...@lists.soe.ucsc.edu> > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > > > _______________________________________________ Genome maillist - Genome@lists.soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/genome
