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
