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Question: Intersect Two File
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gravatar for Aaron Quinlan
8.6 years ago by
Aaron Quinlan • 60
Aaron Quinlan • 60 wrote:
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 gene (boolean yes or no), but I would really like to know __which__ gene the SNP overlaps. Help. Thanks, Aaron
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modified 8.6 years ago by Stuart Andrews • 20 • written 8.6 years ago by Aaron Quinlan • 60
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gravatar for Stuart Andrews
8.6 years ago by
Stuart Andrews • 20
Stuart Andrews • 20 wrote:
Hi Aaron, A two-step solution would be to use the "Fetch closest feature" tool with the set of overlapping SNP's that you obtain from the intersect operation that you describe. The closest feature will be the overlapping gene, and your association will be found. - Stu Stuart Andrews, Ph.D. Postdoctoral Associate Institute for Computational Biomedicine Weill Cornell Medical College, New York, NY
ADD COMMENT • link written 8.6 years ago by Stuart Andrews • 20
You can use "Join the intervals of two queries side-by-side" for this. It's like bedtools intersectBed -wa -wb, I think. Madelaine Gogol Programmer Analyst Stowers Institute To: galaxy-user@bx.psu.edu Subject: Re: [galaxy-user] intersect two file Hi Aaron, A two-step solution would be to use the "Fetch closest feature" tool with the set of overlapping SNP's that you obtain from the intersect operation that you describe. The closest feature will be the overlapping gene, and your association will be found. - Stu Stuart Andrews, Ph.D. Postdoctoral Associate Institute for Computational Biomedicine Weill Cornell Medical College, New York, NY _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy- user
ADD REPLY • link written 8.6 years ago by Gogol, Madelaine • 10
My bad. I have discovered that my two-step solution will not work as I expected, because the "Fetch closest feature" tool only reports upstream and/or downstream features that are *non-overlapping* with the query. Madelaine's suggestion to use the "Join" tool works great! - Stu
ADD REPLY • link written 8.5 years ago by Stuart Andrews • 20
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