Unable To Visualize Peak Data

Question: Unable To Visualize Peak Data

7.3 years ago by

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*

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modified 7.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.3 years ago by Radhouane Aniba • 40

7.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

ADD COMMENT • link written 7.3 years ago by Jennifer Hillman Jackson ♦ 25k

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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

ADD REPLY • link written 7.3 years ago by Jennifer Hillman Jackson ♦ 25k

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