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
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:
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
As you can see from the specifications, bedGraph and interval have
in common, so you can switch between the two when using Galaxy. Double
check the column assignments and making adjustment (if needed) is a
practise (will probably be correct, but just takes a few seconds to
confirm, also done by using the pencil icon).
Tools like "Text Manipulation -> Compute" and "Join, Subtract and
-> Group" are good for generating summary values. The tool group
"Graph/Display Data" also has some graphing tools that may interest
but so does "BEDTools". Bring the data up in Trackster is also an
As you can see, there are plenty of tool options once you start
with interval data!
So hopefully some part of this will help you get to the numbers you
want, in the format most useful.
Galaxy Support and Training