Hi Jennifer,

Intersect_bed is exactly what I need. How can I include this on my workflows? (sorry for asking so many things. Im new with galaxy)

From: Jennifer Jackson [mailto:jen@bx.psu.edu]
Sent: Monday, December 16, 2013 4:03 PM
To: Javier Simon-Sanchez; galaxy-dev@bx.psu.edu
Subject: Re: [galaxy-dev] Count intervals in one file overlapping intervals in another file

Hello Javier,

If you would like to see an enhancement for a tool that is sourced from the tool shed, then the repository author is the correct person to contact. Go to http://usegalaxy.org/toolshed and log in to see contact information. The repo name is "bedtools".

The Tool Shed also has an alternate versions of some BedTools, including this one. An alternative has an option to set overlap length: " bed_intersect".

Also, there are tools in the group "Operate on Genomic Intervals". I don't know the details of your query, but these tools may also be helpful.

Best,

Jen
Galaxy team

On 12/13/13 2:41 AM, Javier Simon-Sanchez wrote:

Hello,

I just noticed that when using the above mentioned option, it is not possible to set a minimum overlap required. This option can be run in the command line version of BEDtools and I think is crucial. Could you please implement it in Galaxy?

Thanks a lot.

-------------------------------------

Javier Simón-Sánchez, PhD

Research Scientist

MRC-Holland

Willem Schoutenstraat 6

1057 DN, Amsterdam

The Netherlands

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