Question: Intersect the intervals of two datasets (Galaxy Version 1.0.0)
gravatar for mdp07vm
6 months ago by
United States
mdp07vm20 wrote:

Hi, I intersected two of my datasets using the 'Intersect the intervals of two datasets (Galaxy Version 1.0.0)' tool. It provided a an output of the intersected intervals but there wasn't any description to the columns (i.e. what they represent) in the tool webpage. Does anyone know what the last 4 columns represent? Also, is the list in output file ranked in anyway?



alignment chip-seq • 248 views
ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson23k • written 6 months ago by mdp07vm20
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson23k wrote:


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

ADD COMMENTlink modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson23k

Excellent. Thanks Jen.


ADD REPLYlink written 6 months ago by mdp07vm20
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