Hello Kristen,

The tool group "BEDTools" has two tools that compare bedGraph file directly: "Merge BedGraph files" and " Intersect multiple sorted BED files". This will get you common and unique intervals.

If you want to do a finer tuned analysis, a bedGraph file that has the leading browser/track lines removed (if present) can be converted to interval format and the tools in the group "Operate on Genomic Intervals" can be used. Help is on the tool forms or you can follow a tutorial that runs through all the tools in protocol 4 in this paper: https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012

Remove extra header lines using "Text Manipulation -> Remove beginning of a file".
Modify the datatype using the dataset's pencil icon to reach the Edit Attributes form.

As you can see from the specifications, bedGraph and interval have much in common, so you can switch between the two when using Galaxy. Double check the column assignments and making adjustment (if needed) is a good practise (will probably be correct, but just takes a few seconds to confirm, also done by using the pencil icon).

http://wiki.galaxyproject.org/Learn/Datatypes#Interval
http://wiki.galaxyproject.org/Learn/Datatypes#BedGraph

Tools like "Text Manipulation -> Compute" and "Join, Subtract and Group -> Group" are good for generating summary values. The tool group "Graph/Display Data" also has some graphing tools that may interest you, but so does "BEDTools". Bring the data up in Trackster is also an option.

As you can see, there are plenty of tool options once you start working with interval data!
So hopefully some part of this will help you get to the numbers you want, in the format most useful.

Best,

Jen
Galaxy team

On 4/11/13 1:36 AM, Kristin Denise Kernohan wrote:
Hi everyone,

I am new to Galaxy and wondering if anyone can help me with a quick question. I have two data sets which are currently in a bedgraph format.  I am looking for a tool to compare between them and find unique or changed sites.  Is there a tool to compare between samples and generate a list of changed sites?

Thank you very much

Kristin 

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