Hi all, 

I think I must be doing something incredibly wrong because it seems that the 
OGI subtract operation has the mirror image problem to intersect.  That is, 
instead of say that my file 1 has (N - 1105) intervals that do not overlap file 
2, it says that N intervals do not overlap.  Do subtract and intersect use the 
same underlying intersection code?  
- Aaron

On Feb 8, 2013, at 10:23 AM, Aaron Quinlan <aaronquin...@gmail.com> wrote:

> Dear list,
> I have a student that found an unexplained discrepancy between the results 
> produced by the "Operate on Genomic Intervals" (OGI) intersect operation 
> versus the OGI join operation.  In particular, we know for certain that there 
> are exactly 1105 intersection of at least 1bp between the two files we are 
> testing, as we have confirmed this with our own bedtools and the ucsc table 
> browser.  An example intersection (intersecting positions: 10012008 - 
> 10012013):
> file 1:
> chr1  10012008        10012021        5.6186
> file 2:
> chr1  10011813        10012013        5_Strong_Enhancer       0       +       
> 10011813        10012013        250,202,0
> However, OGI intersect find 0 intersections between the files (settings: 
> return overlapping intervals, >= 1bp).  In an effort to make sure we didn't 
> goof up on file formats (BED) or genome builds (hg19), we tested the exact 
> same two files with the OGI join operation and found 1105 intersections as 
> expected.
> I also tested the files with the bx-python bed_intersect.py and 
> bed_intersect_basewise.py scripts and get the expected results.
> Does anyone have a suggestion for how to resolve this?
> Thanks for your help and for providing such a fantastic resource to the 
> genomics community.
> Best,
> - Aaron
> quinlanlab.org

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