Question: Intersectbed Provides An Empty Output
gravatar for joanne.lee
7.4 years ago by
joanne.lee0 wrote:


I've downloaded the recent Cygwin version 1.7.24 and an trying to run bedTools but I get an empty file as my output. When I run the same commandline and files on a colleagues computer also through Cygwin I get a file containing the overlaps I seek. is the new Cygwin not compatable with BedTools? I've put the command line we used below:

./intersectbed -a Gene_body.bed -b EdgeR1.bed -wao > yyy.temp

Any help would be appreciated.

bedtools • 2.3k views
ADD COMMENTlink modified 7.4 years ago by Istvan Albert ♦♦ 86k • written 7.4 years ago by joanne.lee0
gravatar for Istvan Albert
7.4 years ago by
Istvan Albert ♦♦ 86k
University Park, USA
Istvan Albert ♦♦ 86k wrote:

Cygwin versions have probably nothing to do with it, but to compile BedTools it needs to have other libraries present

  • make sure that you bedtools was properly compiled on your system and that it actually runs at all - look in the manual, find and test some examples
  • make sure that the files are actually the same, when you transfer them back and forth across Windows machines it is easy to mess up the line endings
ADD COMMENTlink written 7.4 years ago by Istvan Albert ♦♦ 86k

Thanks. Bedtools wasn't installed properly with the GCC compiler and the new commandline is: ./bedtools intersect Not what I was trying.

ADD REPLYlink written 7.4 years ago by joanne.lee0
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