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. Yet in my case, the 5th and 6th columns do not reflect a strand or name --- I suspect the incorrect setting of the strand is the issue. 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 should have realized this sooner. It is strange, however, that intersect is affected by this, yet join is not. 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 >>>> >>>> >>>> >>>> >>>> >>>> ___________________________________________________________ >>>> The Galaxy User list should be used for the discussion of >>>> Galaxy analysis and other features on the public server >>>> at usegalaxy.org. Please keep all replies on the list by >>>> using "reply all" in your mail client. For discussion of >>>> local Galaxy instances and the Galaxy source code, please >>>> use the Galaxy Development list: >>>> >>>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>>> >>>> To manage your subscriptions to this and other Galaxy lists, >>>> please use the interface at: >>>> >>>> http://lists.bx.psu.edu/ >>> >> >
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
