Hi Dan,

Problem solved.  My file2 is a pseudo-BED format from the ENCODE project.  When 
I uploaded it, I explicitly set the type to "bed".  When I do this, intersect 
breaks.  The correct chrom, start, and end columns are selected, but it sets 
stand and name to the 6th and 5th columns, respectively.  In my case, the 
strand is always ".".  If I simply use the "Auto-detect" feature when I upload 
this same file, it works just fine --- name and strand are not set, just chrom, 
start, end.

I suspect this is a rookie mistake on my part and I apologize for clogging the 
airwaves.

Thanks for your help.
- Aaron
quinlanlab.org





On Feb 8, 2013, at 3:15 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote:

> 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 <d...@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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>> 
> 

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