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.kasow...@uconn.edu <mailto:seth.kasow...@uconn.edu>
Beach Hall Room 335 (6-3580)


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