Question: Counting Intervals In One File Overlapping Intervals In Another File - What Are The Hidden Settings?
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gravatar for Mo Heydarian
5.8 years ago by
Mo Heydarian790
United States
Mo Heydarian790 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
bedtools • 806 views
ADD COMMENTlink modified 5.8 years ago by Jennifer Hillman Jackson25k • written 5.8 years ago by Mo Heydarian790
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gravatar for Jennifer Hillman Jackson
5.8 years ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 5.8 years ago by Jennifer Hillman Jackson25k
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 REPLYlink written 5.8 years ago by Alex Shaw10
0
gravatar for Daniel Blankenberg
5.8 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 COMMENTlink written 5.8 years ago by Daniel Blankenberg ♦♦ 1.7k
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