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
