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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