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  • quinlana
    replied
    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.
    Last edited by quinlana; 09-28-2010, 08:33 AM.

    Leave a comment:


  • johnny
    replied
    -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.

    Leave a comment:


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

    Leave a comment:


  • johnny
    replied
    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 ?

    Leave a comment:


  • johnny
    replied
    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

    Leave a comment:


  • mgogol
    replied
    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.

    Leave a comment:


  • johnny
    replied
    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 ?

    Leave a comment:


  • mgogol
    replied
    Do you have data in .bam format?

    Leave a comment:


  • johnny
    started a topic BED Tools Tutorial

    BED Tools Tutorial

    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:

    ###########################

    5.4.1 Usage and option summary

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

    ###########################

    How would on use this command ?

    Thanx a lot in advance!

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