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
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written
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bede.portz
1 answer
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.
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written
by
Istvan Albert
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