User: Aaron Quinlan

gravatar for Aaron Quinlan
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5 years, 9 months ago
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Posts by Aaron Quinlan

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Discrepancy Between Intersect And Join
... 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. ...
written 5.8 years ago by Aaron Quinlan60
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Comment: C: Discrepancy Between Intersect And Join
... 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. ...
written 5.8 years ago by Aaron Quinlan60
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Comment: C: Discrepancy Between Intersect And Join
... 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 direc ...
written 5.8 years ago by Aaron Quinlan60
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Answer: A: Discrepancy Between Intersect And Join
... 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 a ...
written 5.8 years ago by Aaron Quinlan60
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Discrepancy Between Intersect And Join
... 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 ...
bedtools written 5.8 years ago by Aaron Quinlan60 • updated 5.8 years ago by Daniel Blankenberg ♦♦ 1.7k
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Intersect Two File
... Hello, I have a naive question. When using the "Intersect" option in "Operate on Genomic Intervals", is there an option to report the features in the second file that the feature in the first file overlaps? Currently, I am only able to get Galaxy to report that, for example, a SNP overlaps some g ...
galaxy written 8.5 years ago by Aaron Quinlan60 • updated 8.5 years ago by Stuart Andrews20

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