UCSC Intersection Queries

The intersection function of table browser queries allows users to identify overlapping components of 2 different tracks.

To demonstrate the functions of this tool:

• Add a custom track to the Human Mar. 2004 (hg17) assembly using the BED file probes.bed.

• Examine the contents of probes.bed by viewing it in the browser. Note the first line beginning with "track". This controls display and naming of the track.

• View the contents of the custom track in the browser.

Hints: zoom out, toggle display options

• Investigate the contents of the custom track using table browser queries.

Hints: whole genome query, summary/statistics button, toggle output options.
How many entries items are in the custom track?

• To perform an intersection query:
  • Verify that "group" and "track" options point to the custom track.
  • select the "create" button next to "intersection:"

If an intersection query is already in place, the options with be "clear" and "edit"

• Select the following options on the intersect page and click "submit":

• Note the ability to control the degree of intersection (some, none, partial) being selected.

• After intersection is in place, use summary/statistics to count the results and view some in the genome browser.

• Perform the intersection queries between the custom track and the known-genes track and select the output option:

"custom track"

• Observe the impact of the intersection by comparing the IAP_Demo_Track and the intersection results.

Note about intersection direction

The intersection query reports the results in the first set that 
have the intersection you specified with the second set you selected. 

To view the converse, select known genes first, then edit the intersection 
to seek any overlap with custom track. 
How many results are produced when the tracks are inverted?

• Perform the intersection queries between the custom track and the known-genes track and the converse and send the results to the Galaxy.

login to Galaxy.
Check "Send output to Galaxy" in the table browser window.

• See Comparing genomic intervals using galaxy to operate on these results.