Counting Intervals In One File Overlapping Intervals In Another File

Question: Counting Intervals In One File Overlapping Intervals In Another File - What Are The Hidden Settings?

6.3 years ago by

United States

Mo Heydarian ♦ 830 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

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modified 6.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.3 years ago by Mo Heydarian ♦ 830

6.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 -- Jennifer Jackson http://galaxyproject.org

ADD COMMENT • link written 6.3 years ago by Jennifer Hillman Jackson ♦ 25k

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 -- 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

ADD REPLY • link written 6.3 years ago by Alex Shaw • 10

6.3 years ago by

Daniel Blankenberg ♦♦ 1.7k

United States

Daniel Blankenberg ♦♦ 1.7k wrote:

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

ADD COMMENT • link written 6.3 years ago by Daniel Blankenberg ♦♦ 1.7k

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