Count intervals in one file overlapping intervals in another file
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
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Jennifer Hillman-Jackson http://galaxyproject.org
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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org
Javier, This is part of a tool repository that can be installed into a local, cloud, or slipstream Galaxy and used there. http://getgalaxy.org http://usegalaxy.org/cloud https://wiki.galaxyproject.org/BigPicture/Choices http://usegalaxy.org/toolshed https://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uni... I am not sure of the size of your files, but if not too large, these tools may work just fine on a local install on a laptop. For anything larger, a server would be needed for a local or for the easiest set-up, use a cloud. For ongoing work, a slipstream Galaxy can be a great solution for labs. Take care, Jen Galaxy team On 12/16/13 7:30 AM, Javier Simon-Sanchez wrote:
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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
-- Jennifer Hillman-Jackson http://galaxyproject.org
-- Jennifer Hillman-Jackson http://galaxyproject.org
Ok, So I guess I need to install it locally or in the cloud to use certain tools, right? Thanks! From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Monday, December 16, 2013 6:55 PM To: Javier Simon-Sanchez; galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Count intervals in one file overlapping intervals in another file Javier, This is part of a tool repository that can be installed into a local, cloud, or slipstream Galaxy and used there. http://getgalaxy.org http://usegalaxy.org/cloud https://wiki.galaxyproject.org/BigPicture/Choices http://usegalaxy.org/toolshed https://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uni... I am not sure of the size of your files, but if not too large, these tools may work just fine on a local install on a laptop. For anything larger, a server would be needed for a local or for the easiest set-up, use a cloud. For ongoing work, a slipstream Galaxy can be a great solution for labs. Take care, Jen Galaxy team On 12/16/13 7:30 AM, Javier Simon-Sanchez wrote: 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<mailto: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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org -- Jennifer Hillman-Jackson http://galaxyproject.org
participants (2)
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Jennifer Jackson