unable to visualize peak data
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*
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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
participants (2)
-
Jennifer Jackson -
Radhouane Aniba