Question: How to transform Peakzilla output to one that can be displayed in the UCSC Browser
gravatar for bede.portz
4.4 years ago by
United States
bede.portz470 wrote:

I have used Peakzilla to call peaks on some ChIP-seq data, and would now like to visualize this data on the UCSC (or other) genome browser. I am unsure of the ideal way to display this data.  It could be turned into a .bed file, but the output of peakzilla isn't in a file format I recognize. I want to maximze the amount of information I retain when re-formatting the file to a format suitable for UCSC .

Example of the file format:

#Chromosome    Start    End    Name    Summit    Score    ChIP    Control    FoldEnrichment    DistributionScore    FDR
chr1    4785576    4785728    Peak_1420    4785652    3.09    3.23    0.07    43.74    0.98    5.59
chr1    4785747    4785899    Peak_4838    4785823    1.84    1.92    0.08    23.81    1.00    2.06
chr1    4807591    4807743    Peak_2099    4807667    2.68    2.75    0.07    37.35    1.00    3.89


ADD COMMENTlink modified 4.4 years ago by Istvan Albert ♦♦ 79k • written 4.4 years ago by bede.portz470
gravatar for Istvan Albert
4.4 years ago by
Istvan Albert ♦♦ 79k
University Park, USA
Istvan Albert ♦♦ 79k wrote:

We'll you can't really maximize the information if the format that you need to turn it into only has say one column for values then that's about it.

This data seems to be suited for bedgraph format. You can cut the columns according the order and remove the comment lines.

You may need to create a different bedgraph for each of the columns that you want to display.

ADD COMMENTlink written 4.4 years ago by Istvan Albert ♦♦ 79k
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