18 months ago by
The data is not sorted (ranked) by the tool. Also, the output columns are in same order as originally given.
From the tool form help ("Syntax" section for this tool):
Overlapping Intervals returns entire intervals from the first dataset that overlap the second dataset. The returned intervals are completely unchanged, and this option only filters out intervals that do not overlap with the second dataset.
Overlapping pieces of Intervals returns intervals that indicate the exact base pair overlap between the first dataset and the second dataset. The intervals returned are from the first dataset, and all fields besides start and end are guaranteed to remain unchanged.
The chrom (aka chromosome), start, and end position are the minimum defined columns for interval formatted input data. Other defined columns can include name and strand. Other undefined columns (meaning: do not describe a specific metadata attribute) can be any alphanumeric content, tab-delimited, that you wish to include. These attribute assignments can be modified by clicking on the "pencil" icon for a dataset to reach the Edit Attributes forms.
If you need more help, please let us know. Thanks! Jen, Galaxy team