BED Tools Tutorial

[johnny]

Sorry I'm a total beginner in bioinformatics and really need some help.

I'm on a mac and so far I've managed to install xcode and therefore was able to execute the installation process described here: http://code.google.com/p/bedtools/

Now I've got the problem that I can't get anything started because I'm lacking the 'terminal' commands. So here I picked an example from the manual:

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5.4.1 Usage and option summary

Usage: $ bamToBed [OPTIONS] -i <BAM>

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How would on use this command ?

Thanx a lot in advance!

[mgogol]

Do you have data in .bam format?

[johnny]

Yes, but do I have to give the full path to the files or in which directory do I have to place them ?
Which directory do I have to open in terminal, when I execute a command ?

[mgogol]

You can either give the full path to the files or work in the same directory as the files. You can call a command from any directory if it's installed somewhere in your PATH.

[johnny]

I told you I'm an absolute beginner, but finally I've solved the problem.
When I copied an example command like: $ bamToBed [OPTIONS] -i <BAM> I didn't remove the '$' so I had 2 '$' in the terminal which led to a 'command not known'. But now it works so I'll finally get back to you with some other basic usage questions

[johnny]

Okay, as proposed here is my next question.
When I use the coverageBed command, it gives me only the coverage for the specified regions in file b but not of the whole span. E.g. reference file b contains chr1: 1000-2000 , then I only get the mean coverage for this region. How can I get the per base coverage in this region ?

[quinlana]

Use the -d option for per base coverage. Available in version 2.9 and later.
Aaron

[johnny]

-d is what I used. The problem is, if in the reference b file are given e.g. 5 ranges like described before, I only get one value per each range. What I would like to have is for every base in the range. In this case: chr1: 1000-2000 I would expect 1000 lines of output.

[quinlana]

That is odd. Could you post the command you used and the output?
Section 5.9.6 of the manual illustrates the way the output should loo.