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
