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I was wondering if Galaxy can be used to call peaks? I have not seen anything that looks like a Peak Calling Algorithm. But..I was thinking that one could use the subtract function to enrich the data. For example, one could take the dataset from a ChIPseq of a given protein and subtract out the corresponding Igg control. The genomic intervals that remain should be very strong candidates for actual sites.
Which brings me to another question, how does the subtract function work exactly? To illustrate what I'm trying to figure out, an example. Lets look at a single genomic location in dataset 1 that has 10 reads within it. Then take a second dataset that has 1 read in the same genomic location. Would the subtract function give zero reads in the new file? Or would it have 9 reads in the new file? I suppose another way to phrase the question, is, is the subtraction function qualitative or quantitative?
Which brings me to another question, how does the subtract function work exactly? To illustrate what I'm trying to figure out, an example. Lets look at a single genomic location in dataset 1 that has 10 reads within it. Then take a second dataset that has 1 read in the same genomic location. Would the subtract function give zero reads in the new file? Or would it have 9 reads in the new file? I suppose another way to phrase the question, is, is the subtraction function qualitative or quantitative?
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