Hello Seth, It sounds like there may be also reads joining with more than one exon - so there is a many-to-many relationship in the output. This would not be uncommon (especially if there are multiple reads per gene cluster) and would result in an input read being reported >1 time in the output. Depending on the data, separating the join into two by strand and/or increasing the overlap may be appropriate. FAQ/Screencast: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations Hopefully this helps, Jen Galaxy team On 8/6/11 6:21 AM, Seth Kasowitz wrote:

Hello, 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 reads. 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

-- Seth Kasowitz University of Connecticut Department of Molecular and Cellular Biology seth.kasowitz@uconn.edu <mailto:seth.kasowitz@uconn.edu> Beach Hall Room 335 (6-3580)

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