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

On May 13, 2010, at 4:32 PM, Aaron Quinlan 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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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

On May 14, 2010, at 2:01 PM, Gogol, Madelaine wrote:

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

-----Original Message----- From: galaxy-user-bounces@lists.bx.psu.edu [mailto:galaxy-user-bounces@lists.bx.psu.edu ] On Behalf Of Stuart Andrews Sent: Friday, May 14, 2010 12:46 PM 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

On May 13, 2010, at 4:32 PM, Aaron Quinlan 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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