Hello again Tian, Unfortunately the errors you are finding are present in the files provided by the contributors and you will have to take these issues up with them directly. If you experience subsequent browser related issues please feel free to contact the mailing list again.
Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 7/25/12 12:26 PM, tian chi wrote: > Hi Steve, > This is a nightmare. It makes the data useless for the many people lacking > access to UNIX/Linux. And even for people who do, they will have to check > each of the chromosomes. Why so awkward? Is there a better way to do this? > > Tx > Tian. > > ------ Forwarded Message >> From: Steve Heitner <[email protected]> >> Reply-To: <[email protected]> >> Date: Wed, 25 Jul 2012 11:59:53 -0700 >> To: 'tian chi' <[email protected]>, <[email protected]> >> Subject: RE: [Genome] <no subject> >> >> Hello, Tian. >> >> I looked at the page you referenced and it is indeed an mm8 file. The file >> is merely a text file which can be edited like any other text file. Simply >> remove the line that specifies chr4:155029799. The only problem is that it >> is a very large text file. If you're working in Windows, most Windows text >> editors (including Microsoft Word) don't work very well with large text >> files, so you would need to search the web for a large text file editor. If >> you're working in UNIX or Linux, it should be fairly easy to edit the file >> at the command line using a UNIX-based text editor. Just be aware that this >> may not be the only chromosome coordinate violation in the file. It was >> displaying the chr4 error because it was the first one that it encountered, >> but once you remove the chr4-specific line, you may find when you try to >> load your custom track again that you need to remove other lines as well. >> >> Please contact us again at [email protected] if you have any further >> questions. >> >> --- >> Steve Heitner >> UCSC Genome Bioinformatics Group >> >> -----Original Message----- >> From: tian chi [mailto:[email protected]] >> Sent: Wednesday, July 25, 2012 10:37 AM >> To: [email protected] >> Subject: Re: [Genome] <no subject> >> >> >> The way I uploaded the file was correct. I contacted the authors of the >> paper, and got the following response: >> >>> 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. >>> >>> I am sorry that these data were processed using an earlier version of >>> SICER algorithm and such issue was not well taken care of. And the >>> UCSC genome browser has also been updated to intolerant of these >>> problems. Sorry for the inconvenience. >> However, I do not know how to do this exactly. >> >> >> The link to the data: >> >> http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/cd4k4k27/ >> >> Pls upload the last sample (Th-Naïve, H3K27me3, summary bed file >> >> >> Thanks >> Tian >> >>> From: Steve Heitner <[email protected]> >>> Reply-To: <[email protected]> >>> Date: Wed, 25 Jul 2012 10:26:10 -0700 >>> To: 'tian chi' <[email protected]>, <[email protected]> >>> Subject: RE: [Genome] <no subject> >>> >>> Hello, Tian. >>> >>> Can you please provide the source URL for this file? As with the >>> previous similar error you encountered, it appears that you may be >>> trying to load this file into the wrong assembly. >>> >>> Please contact us again at [email protected] if you have any further >>> questions. >>> >>> --- >>> Steve Heitner >>> UCSC Genome Bioinformatics Group >>> >>> -----Original Message----- >>> From: [email protected] [mailto:[email protected]] >>> On Behalf Of tian chi >>> Sent: Tuesday, July 24, 2012 4:36 PM >>> To: [email protected] >>> Subject: [Genome] <no subject> >>> >>> Hi >>> I am trying to upload a ChIP-seq file into the Custom Track, but got >>> this error message: >>> >>> Error File 'mm8-Th-naive-H3K27me3_summary.graph' - Error line 1117090 >>> of custom track: chromEnd larger than chrom chr4 size (155029799 > >> 155029701). >>> This prevents me from proceeding any further. Any ideas how to get >>> round this? >>> >>> Thanks, >>> Tian >>> >>> >>> >>> _______________________________________________ >>> 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
