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 > > > > > > > >
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