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Old 03-13-2013, 05:41 AM   #1
sarah_19
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Location: London

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Default Bedtools command not found

I have downloaded BamTools 2.17.0 onto my mac OS X 10.5.8 and installed using terminal

I copied all files I want to work with into the bin folder

When in terminal I moved into the bin folder

I can see bedtools

if I manually drag bedtools into the terminal it gives me a description of all the things it can be used for

however anything I type in gets a 'command not found error'

I am trying to run the line
bedtools coverage -hist -abam sample6.bam -b ampfinal.bed >result.txt

when I type this I get:
-bash: bedtools: command not found
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Old 03-13-2013, 06:06 AM   #2
cormicp
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Sounds like the folder containing Bedtools might not be in your PATH environment variable

Try ./bedtools coverage -hist -abam sample6.bam -b ampfinal.bed >result.txt when in the bin folder to see if it works.

If it does you can simply add this folder to your PATH and you should be able to call it from any directory.
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Old 03-13-2013, 08:51 AM   #3
sarah_19
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Ah such a simple answer
Thank you so much it worked
Sarah
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