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
