I have predicted CNV regions from 3 different tools. I want to check the overlapping regions between the tools. Should I use the Galaxy intersect option or overlap option? What is the difference between the two?
These are basically the same function. The differences will be with the different tool options, including alternatives ways to filter/report the final output. These compare two datasets, not three, so do pairwise comparisons first, then use other functions to merge the data together in a custom tabular dataset that can be manipulated further.
The tools in groups Operate on Genomic Intervals and BEDTools have example use cases per function described directly on the tool forms. For basic data manipulation after, start with tools in the group Text Manipulation or search by keyword(s) in the tool panel. Most are tagged with analogous Unix functions (cut, head, sort, and the like). Tools in the groups Datamash, Filter and Sort, Join, Subtract and Group are often used with Text Manipulation tools in combination to create custom data reduction queries.
I would suggest reviewing the examples for the different functions, running a few that seem like a fit, and comparing to see which produces the most useful output format/content for any downstream manipulations/tools/visualizations you wish to use.
Thanks! Jen, Galaxy team