Hi Aaron,
If you did this on our public main server, you can use the share options (gear icon in history list --> Share or publish), this will let us investigate a bit deeper into the exact problem/situation.
If you were using a local instance (or the public server), then emailing them directly to me will work just fine.
Thanks for using Galaxy,
Dan
On Feb 8, 2013, at 3:10 PM, Aaron Quinlan wrote:
Hi Dan,
Thanks for the follow up. Yes, I was also able to get it to work when I created a test case using the example I originally sent. Yet when I run the entire files, I get zero intersections. Join, in contrast, works fine. I'd be happy to share the files. Would it be best to send them directly to you by email? The are small.
Thanks much for the help,
- Aaron
quinlanlab.org
On Feb 8, 2013, at 2:56 PM, Daniel Blankenberg dan@bx.psu.edu wrote:
Hi Aaron,
I just tested this small example and it reported one region as the result of the intersect: https://main.g2.bx.psu.edu/u/dan/h/aaron-quinlan-intersect-test-02-08-2013
Do you have a history available that you can share (privately if you desire) where you see the issue, and we'll take a look.
Thanks for using Galaxy,
Dan
On Feb 8, 2013, at 10:23 AM, Aaron Quinlan 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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