Hello Suman, For each seperate track, adjust the color settings with the "color" attribute in the track line. The three numbers refer to standard RGB color maps. A google search can bring up examples of colors with the corresponding numbers to use.
FAQ explaining this and related track line attributes: http://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK Best, Jen UCSC Genome Browser Support On 9/9/10 8:48 AM, suman pal wrote: > > Dear Al, > > Kindly advise me how to change the colour of the BedGraph file in the > histogram view in UCSC browser. > Currently,I am getting a green coloured histogram. My settings are: > color=0,128,0 visiblity=full, which turns out to be greeen. > > For individual bedfiles I want to have separate colours like blue and red. > Can you guys suggest me a way of doing that. > > Thanks. > > Suman > > --- On Wed, 9/8/10, Jennifer Jackson<[email protected]> wrote: > >> From: Jennifer Jackson<[email protected]> >> Subject: Re: [Genome] conversion of Bedfile to BedGraph problem >> To: "suman pal"<[email protected]> >> Cc: [email protected] >> Date: Wednesday, September 8, 2010, 12:25 AM >> Hello Suman, >> >> There is a pre-compiled executable available named >> bedItemOverlapCount >> (same utility as named below, in the forwarded email). >> >> Ftp from the source downloads area: >> http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ >> >> If there was some problem that you already encountered with >> the >> bedItemOverlapCount utility, would you be able to clarify? >> >> Please continue to use the mailing list [email protected] >> for followup >> so that our entire team can help contribute to >> troubleshooting the issue. >> >> Regards, >> >> Jen >> UCSC Genome Browser Support >> >> On 9/6/10 10:03 PM, suman pal wrote: >>> Dear All, >>> >>> I need some help in converting the bed file into >> BedGraph.Kindly see the attached bed file and could you >> please send some command lines to process such files and >> visualizing them in UCSC Genome Browser.Please see the >> message below for reference. >>> >>> Sincerely >>> Suman >>> >>> >>> --- On Sat, 9/4/10, suman pal<[email protected]> >> wrote: >>> >>>> From: suman pal<[email protected]> >>>> Subject: Re: [Genome] Request for ways to >> visualize gff3 Chip on chip data in UCSC browser >>>> To: "Mary Goldman"<[email protected]> >>>> Date: Saturday, September 4, 2010, 11:48 AM >>>> According to your instruction I have >>>> converted a part of my gff3 for chr4 into bed file >> as >>>> nim.bed. However, I am facing difficulty in the >> next step. >>>> i.e. converting it into a BedGraph. >>>> In the directory i have reached the bed item >> overlap count >>>> and downloaded it but I am unable to run it in my >> PC. >>>> >>>> Kindly take a look at the attached file.It will be >> helpful >>>> if you can suggest some steps in more detail. >>>> >>>> sincerely >>>> Suman >>>> >>>> --- On Sat, 9/4/10, Mary Goldman<[email protected]> >>>> wrote: >>>> >>>>> From: Mary Goldman<[email protected]> >>>>> Subject: Re: [Genome] Request for ways to >> visualize >>>> gff3 Chip on chip data in UCSC browser >>>>> To: "suman pal"<[email protected]> >>>>> Cc: [email protected] >>>>> Date: Saturday, September 4, 2010, 3:35 AM >>>>> Hi Suman, >>>>> >>>>> Unfortunately, GFF3 files are not supported as >> custom >>>>> tracks for the >>>>> genome browser. We recommend converting your >> GFF3 file >>>> to a >>>>> bed (more >>>>> information can be found here: >>>>> http://genome.ucsc.edu/FAQ/FAQformat.html#format1). >>>>> Once you have >>>>> converted it you can use the >> bedItemOverlapCount >>>> utility >>>>> (http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads >>>>> in >>>>> "Other executable binary utilities") to build >> a >>>> bedGraph, >>>>> which will >>>>> allow you to see the peaks. >>>>> >>>>> Please feel free to contact the mail list >> again if >>>> you >>>>> require further >>>>> assistance. >>>>> >>>>> Best, >>>>> Mary >>>>> ------------------ >>>>> Mary Goldman >>>>> UCSC Bioinformatics Group >>>>> >>>>> On 9/1/10 7:16 AM, suman pal wrote: >>>>>> Dear Sir/madam, >>>>>> >>>>>> I am postdoctoral fellow working in CCMB, >>>>> Hyderabad,India in the laboratory of >> Functional >>>> Genomics and >>>>> Gene Silencing Group. >>>>>> >>>>>> I will be highly obliged if you kindly >> suggest me >>>> some >>>>> steps to display my gff3 Nimblegen ChIP on >> Chip >>>> genome >>>>> tiling array files in the UCSC genome >> Browser.The >>>> organisms >>>>> is Drosophila Melanogaster (dm3 rel5). >>>>>> >>>>>> When I am adding the gff3 files in custom >> track >>>> the >>>>> track is looking inverted to me. Is there any >> way to >>>> change >>>>> this view. >>>>>> >>>>>> Most importantly Is there any way I can >> display >>>> the >>>>> peak scores or log2 ratios as well. >>>>>> >>>>>> >>>>>> Looking forward to your reply. >>>>>> >>>>>> Sincerely, >>>>>> Suman Pal, >>>>>> Laboratory for Gene Silencing and >> Functional >>>> Genomics >>>>>> G-110, South wing, ground floor, >>>>>> CCMB,Hyderabad,India >>>>>> >>>>>> >>>>>> >>>>>> >> _______________________________________________ >>>>>> 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
