Hi Rad,

Thanks for sharing your history.

The problem is with the database coordinates being out of range of the actual chromosome length, as compared to the UCSC Browser. Some programs will do this if the data overhangs the ends. So, to help display, specifically change:

1) the first row = change the start to be "0"

2) the last row = change the end to be "247249719"

This is for hg18 chr1. If you have other data, the start would also need to be "0", but the end would have to be whatever that chromosomes length is at UCSC. To capture the lengths, using the UCSC Browser, on the gateway page for an assembly is a link called "Sequences" (at the end of the full name, start of description text). Is a quick way to see the lengths, but you can also pull the "chromInfo" table out of the Table Browser.

Glad we could help,

Jen
Galaxy team


On 8/15/11 8:26 AM, Jennifer Jackson wrote:
Hello Rad,

It is difficult to tell without seeing your data. Would you like to
share a history link? Use "Options -> Share or Publish", generate the
link, and email it back directly to me (not the mailing list). In your
email, also please note the dataset number with the display problem.

Hopefully we can help,

Jen
Galaxy team

On 8/15/11 7:52 AM, Radhouane Aniba wrote:
Hi everyone,

I have a bed file with reads mapped on the genome, I filtered it to have
just chr1, once I got the filtered file, I run MACS on it to calculate
peaks (btw it is a histone modification mapped reads) and the file was
generated successfully

when I tried to view it in UCSC genome browser I got an error message

* Error 500: Internal Server Error**

Is this related to galaxy or UCSC GB ? I tried the experiment 4 times
and it is always the case

Cheers

Rad
*
--
*R. Aniba*
/Bioinformatics Postdoctoral Research Scientist/
*Institute for Advanced Computer Studies
Center for Bioinformatics and Computational Biology* *(CBCB)*
*University of Maryland, College Park
MD 20742*



___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

http://lists.bx.psu.edu/


--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

Reply via email to