Thanks for the reply. I am using Galaxy to upload gff3 files and convert it to Bed and Bedgraph (Greg Hannon BedTools)for visualization in the UCSC browser.
sincerely Suman --- On Wed, 9/15/10, 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 15, 2010, 11:18 PM > Hello Suman, > > The compiled utilities from here: > > http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ > > only will work on that type of system, not a PC. You could > try > downloading the source code and compiling for a PC, but we > cannot offer > detailed support. Also please be aware that not all > utilities will run > on smaller machines as they require more memory/processing > capacity. > Source: > http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads > > A web version also exists in the Galaxy tool kit (http://usegalaxy.org). > You can send an uploaded custom track to Galaxy using the > table browser > (check the "Galaxy" box at output) or upload directly > there, convert the > file, then send back to the UCSC browser as a custom > track. > > Hopefully one of these solutions will work, > > Jen > UCSC Genome Browser Support > > On 9/14/10 11:39 PM, suman pal wrote: > > Hello, > > > > I think the Windows environment of my PC is not > allowing the program to download bedItemOverlapCount > properly from the UCSC site. Thus it cannot run the file in > the Windows environment. Is there any way I can bypass the > file problem using some command prompts. > > > > Alternatively, if I just add the following lines in > the text editor of the bed file and directly upload as > custom track will it work ! e.g. > > > > #sort bedFile.bed | bedItemOverlapCount > [options]<dm3> stdin > > browser position chr4:0-7164 > > chr4 0 > 245 3.39 > > chr4 690 > 1230 3.14 > > chr4 713 > 1258 3.31 > > chr4 1575 > 2130 2.84 > > chr4 1932 > 3506 3.39 > > chr4 2310 > 2645 3.21 > > chr4 2805 > 3265 3.06 > > chr4 3615 > 4060 3.81 > > chr4 3861 > 4306 3.17 > > chr4 4927 > 5160 2.91 > > chr4 4970 > 5420 2.43 > > chr4 6451 > 7321 3.06 > > chr4 6619 > 7164 3.24 > > > > > > looking forward to your reply. > > 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
