Hi Steve, That image was not correct, which, according to the authors , is because I uploaded the wrong file. So ignore that email, but pls address the following instead:
> The simple way is to remove that line from the file. You can search > for 155029799 and delete that line. It is at the end of a chromosome so it > will not affect the biological results. How exactly should I do this? Tx Tian ------ Forwarded Message > From: Steve Heitner <[email protected]> > Reply-To: <[email protected]> > Date: Wed, 25 Jul 2012 10:51:37 -0700 > To: 'tian chi' <[email protected]>, <[email protected]> > Subject: RE: [Genome] <no subject> > > Hello, Tian. > > The image you sent looks exactly as we would expect to see a BED file > containing ChIP-seq peak data. > > Please contact us again at [email protected] if you have any further > questions. > > --- > Steve Heitner > UCSC Genome Bioinformatics Group > > On 7/23/12 5:05 PM, tian chi wrote: >> Hi Roe, >> I upload a Bed file containing ChIP-seq data, which should be displayed > as peaks. Instead, I got the following. Pls help out! >> Tx >> Tian > > -----Original Message----- > From: [email protected] [mailto:[email protected]] On > Behalf Of Greg Roe > Sent: Tuesday, July 24, 2012 11:55 AM > To: tian chi; [email protected] > Subject: Re: [Genome] <no subject> > > Hi Tian, > > GSM361998 is actually mapped to the mm8 mouse assembly. Perhaps you were > trying to upload the custom track on mm9/10? The would definitely explain > the error. Select mm8 from the Gateway page > (http://genome.ucsc.edu/cgi-bin/hgGateway) and see if that works. > > Please let us know if you have any additional questions: [email protected] > > - > Greg Roe > UCSC Genome Bioinformatics Group > > > > > On 7/23/12 5:05 PM, tian chi wrote: >> Re: [Genome] <no subject> * Hi Greg, >> Just found I could not upload a BED file either. The file name is >> GSM361998, from the following site: >> >> http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM361998 >> >> I tried to upload, and got the following error message: >> >> Error File 'GSM361998.bed' - Error line 662 of custom track: chromEnd >> larger than chrom chr2 size (181847110 > 181748087) >> >> I also got such a message when loading with another file. So it seems >> your program is acting up. >> >> Thanks >> Tian >> * >> >> ---------------------------------------------------------------------- >> -- >> *From: *Greg Roe <[email protected]> >> *Date: *Mon, 23 Jul 2012 16:51:48 -0700 >> *To: *tian chi <[email protected]> >> *Cc: *<[email protected]> >> *Subject: *Re: [Genome] <no subject> >> >> Hi Tian, >> >> >> >> That is a bigBed file. We tested from here using NCBI link (via >> bigDataUrl), but got a byte-range request error, so NCBI apparently >> don't support doing that. >> >> >> You will have to download the file and figure out where to host it >> yourself to create the custom track. >> >> >> Please let us know if you have any additional questions: >> [email protected] >> >> - >> Greg Roe >> UCSC Genome Bioinformatics Group >> >> >> >> >> On 7/23/12 12:47 PM, tian chi wrote: >> >> >> >> Hi, >> I have a problem adding a custom track. The data (in bb format) >> are located >> below: >> >> http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM774289 >> >> I downloaded the data into my computer. When I tried to upload it >> to the Add >> Custom Tracks page, I got an error message saying " can not read >> the bb >> file". >> >> Pls help out! >> >> Thanks a lot >> Tian >> >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> >> >> > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > ------ End of Forwarded Message _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
