Counting intervals in one file overlapping intervals in another file - what are the hidden settings?
Hi, I am using the "Count intervals in one file overlapping intervals in another file" tool (part of the bedTools package) to assess the number of RNA-seq reads that map back to a specific region. (I am using this on the Galaxy test server). I am finding that this tool returns many more reads than it should. In reading the bedTools manual, it seems like this tool is the "windowBed" tool and it actually has many more parameters that are not shown on the Galaxy interface. What are these (hidden) settings for these parameters that are not shown? Hopefully this can explain my incorrectly recorded reads. Thanks in advance. Cheers, Mo Heydarian
Hello Mo, This tool comes from a repository sourced from the Tool Shed: http://toolshed.g2.bx.psu.edu/ Search for a tool named "bedtools" with owner "aaronquinlan". You could examine the repository and then the tool wrapper author can be contacted directly with questions about parameters or if you think there is a bug. Hopefully this helps! Jen Galaxy team On 8/16/12 10:13 AM, Mohammad Heydarian wrote:
Hi, I am using the "Count intervals in one file overlapping intervals in another file" tool (part of the bedTools package) to assess the number of RNA-seq reads that map back to a specific region. (I am using this on the Galaxy test server). I am finding that this tool returns many more reads than it should.
In reading the bedTools manual, it seems like this tool is the "windowBed" tool and it actually has many more parameters that are not shown on the Galaxy interface. What are these (hidden) settings for these parameters that are not shown?
Hopefully this can explain my incorrectly recorded reads.
Thanks in advance.
Cheers, Mo Heydarian
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
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-- Jennifer Jackson http://galaxyproject.org
Hi, I'm also interested in using bedtools with galaxy. I have found a bug. When I try to run "Intersect multiple sorted BED files" Error: The requested genome file (/galaxy/home/g2test/galaxy_test/tool-data/shared/ucsc/chrom/hg_g1k_v37.len) could not be opened. Exiting! I've used bedtools on the command line, and it is looking for a file that specifies the chr length for the reference genome. Alex On 17 August 2012 08:23, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hello Mo,
This tool comes from a repository sourced from the Tool Shed: http://toolshed.g2.bx.psu.edu/
Search for a tool named "bedtools" with owner "aaronquinlan". You could examine the repository and then the tool wrapper author can be contacted directly with questions about parameters or if you think there is a bug.
Hopefully this helps!
Jen Galaxy team
On 8/16/12 10:13 AM, Mohammad Heydarian wrote:
Hi, I am using the "Count intervals in one file overlapping intervals in another file" tool (part of the bedTools package) to assess the number of RNA-seq reads that map back to a specific region. (I am using this on the Galaxy test server). I am finding that this tool returns many more reads than it should.
In reading the bedTools manual, it seems like this tool is the "windowBed" tool and it actually has many more parameters that are not shown on the Galaxy interface. What are these (hidden) settings for these parameters that are not shown?
Hopefully this can explain my incorrectly recorded reads.
Thanks in advance.
Cheers, Mo Heydarian
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Alex Shaw Research Officer Neuroscience Research Australia www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1112 F +61 2 9399 1005
Hi Alex, This error has been corrected, thanks for reporting it. Please let use know if you encounter any additional issues. Thanks for using Galaxy, Dan On Aug 21, 2012, at 1:12 AM, Alex Shaw wrote:
Hi,
I'm also interested in using bedtools with galaxy. I have found a bug. When I try to run "Intersect multiple sorted BED files"
Error: The requested genome file (/galaxy/home/g2test/galaxy_test/tool-data/shared/ucsc/chrom/hg_g1k_v37.len) could not be opened. Exiting!
I've used bedtools on the command line, and it is looking for a file that specifies the chr length for the reference genome.
Alex
On 17 August 2012 08:23, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hello Mo,
This tool comes from a repository sourced from the Tool Shed: http://toolshed.g2.bx.psu.edu/
Search for a tool named "bedtools" with owner "aaronquinlan". You could examine the repository and then the tool wrapper author can be contacted directly with questions about parameters or if you think there is a bug.
Hopefully this helps!
Jen Galaxy team
On 8/16/12 10:13 AM, Mohammad Heydarian wrote:
Hi, I am using the "Count intervals in one file overlapping intervals in another file" tool (part of the bedTools package) to assess the number of RNA-seq reads that map back to a specific region. (I am using this on the Galaxy test server). I am finding that this tool returns many more reads than it should.
In reading the bedTools manual, it seems like this tool is the "windowBed" tool and it actually has many more parameters that are not shown on the Galaxy interface. What are these (hidden) settings for these parameters that are not shown?
Hopefully this can explain my incorrectly recorded reads.
Thanks in advance.
Cheers, Mo Heydarian
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Alex Shaw Research Officer
Neuroscience Research Australia
www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1112 F +61 2 9399 1005 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (4)
-
Alex Shaw -
Daniel Blankenberg -
Jennifer Jackson -
Mohammad Heydarian