subtractbed error

[GoogleCodeExporter]

What steps will reproduce the problem?
1.subtractBed -a file1 -b file2 > output.bed
2.if file1=10 peaks, if file2=5 peaks 
3.problem with output peak numbers.

What is the expected output? What do you see instead?
when peaks from file1 are subtracted from file2 the output has more peaks than 
file1. 

What version of the product are you using? On what operating system?
bedtools v2.16.2 Linux Ubuntu 12.04

Please provide any additional information below.

Original issue reported on code.google.com by har...@students.iiserpune.ac.in on 1 Oct 2012 at 5:58

[GoogleCodeExporter]

I need more detail to understand the problem.  Could you provide examples of 
what you are seeing versus what you expect to see?

Original comment by aaronqui...@gmail.com on 22 Oct 2012 at 8:20

[GoogleCodeExporter]

I wanted to find out all the common regions from file a (expt).bed and file
b (control).bed and then remove these regions completely from file a. but
the subtractbed program compares regions and retains non matching portions
of the region. Please let me know is there a setting or bedtool to remove
common regions completely. thanks

-- 
Mr.SHREE HARSHA T T.
Senior Research Fellow
Prof L S Shashidhara's Lab
Department of Biology, III Floor,
Sai Trinity Building, Central Tower,
Indian Institute of Science Education and Research ( IISER Pune)
Garware Circle, Pashan,
PUNE-411021, Maharashtra , India

Email:    harsha@students.iiserpune.ac.in
Phone:  91-20-2590 8066
Fax :      91-20-2589 9790

Original comment by har...@students.iiserpune.ac.in on 23 Oct 2012 at 7:13

[GoogleCodeExporter]

At least in bedtools v2.17.0 you have the -A option:

subtractBed -a file1 -b file2 -A > output.bed

    -A  Remove entire feature if any overlap.  That is, by default,
        only subtract the portion of A that overlaps B. Here, if
        any overlap is found (or -f amount), the entire feature is removed.

Original comment by hulselma...@gmail.com on 6 Dec 2013 at 10:43