I am hoping for some clarification on how Join on Genomic Intervals
functions. I have two lists of intervals: mapped reads and a list of exons.
If I join the two (INNER JOIN), I expect multiple reads to join with the
same exon, and see this in the output. What is confusing me is that some
output has more joined intervals returned than were present in the input
For example: I join 17,000,000 mapped reads with a list of 300,000 exons and
retrieve 21,000,000 joined intervals

I must be misunderstanding what the function does, and am hoping someone can
explain how the output can have more lines than the reads submitted.

Thank you,

Seth Kasowitz
University of Connecticut
Department of Molecular and Cellular Biology
Beach Hall Room 335 (6-3580)
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