Using Galaxy to Call Peaks?

[Giles]

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?

[mgogol]

I don't think Galaxy has anything that could be called a peak-calling algorithm built in (yet). You could do something crude by filtering for a certain height and merging those regions together, but a peak calling algorithm actually designed for Chip-seq data will likely give you better results.

You could try MACS. You do have to run it from the command line, but you might as well give up and dive into this command line stuff if you're working with high-throughput sequencing data.

I'm pretty sure the galaxy subtract function would return 0 reads in the new file, but if you're not sure about something like that, you could always test it out.

[Giles]

Test

I am going to do that today by creating a small file that has multiple hits at one genomic interval and 1 hit at another. I'll post what I find out.

[Chipper]

If you want a GUI for peak calling you can try Sole-search (http://chipseq.genomecenter.ucdavis....in/chipseq.cgi) or Cisgenome.

[Giles]

uc davis genome center

I tried to use the uc davis genome center software, and the tool that is used to call peaks seems to be corrupted. Has anyone used it lately? there is no contact information listed for help.