BED Tools Tutorial

johnny · 08-25-2010, 07:50 AM

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!

mgogol · 08-25-2010, 10:13 AM

Do you have data in .bam format?

johnny · 08-25-2010, 10:45 AM

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 · 08-25-2010, 11:11 AM

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 · 08-26-2010, 02:57 AM

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 · 09-28-2010, 01:37 AM

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 · 09-28-2010, 05:55 AM

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

johnny · 09-28-2010, 06:03 AM

-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 · 09-28-2010, 06:07 AM

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.

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08-25-2010, 07:50 AM	#1
johnny Member Location: Germany Join Date: Dec 2009 Posts: 15	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!

09-28-2010, 06:07 AM	#9
quinlana Senior Member Location: Charlottesville Join Date: Sep 2008 Posts: 119	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 at 09:33 AM.

08-25-2010, 10:13 AM	#2
mgogol Senior Member Location: Kansas City Join Date: Mar 2008 Posts: 197	Do you have data in .bam format?

08-25-2010, 10:45 AM	#3
johnny Member Location: Germany Join Date: Dec 2009 Posts: 15	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 ?

08-25-2010, 11:11 AM	#4
mgogol Senior Member Location: Kansas City Join Date: Mar 2008 Posts: 197	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.

08-26-2010, 02:57 AM	#5
johnny Member Location: Germany Join Date: Dec 2009 Posts: 15	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

09-28-2010, 01:37 AM	#6
johnny Member Location: Germany Join Date: Dec 2009 Posts: 15	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 ?

09-28-2010, 05:55 AM	#7
quinlana Senior Member Location: Charlottesville Join Date: Sep 2008 Posts: 119	Use the -d option for per base coverage. Available in version 2.9 and later. Aaron

09-28-2010, 06:03 AM	#8
johnny Member Location: Germany Join Date: Dec 2009 Posts: 15	-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.