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Question: Intersectbed Provides An Empty Output
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gravatar for joanne.lee
5.3 years ago by
joanne.lee • 0
joanne.lee • 0 wrote:

Hi,

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 • 1.7k views
ADD COMMENT • link •
modified 5.3 years ago by Istvan Albert ♦♦ 78k • written 5.3 years ago by joanne.lee • 0
0
gravatar for Istvan Albert
5.3 years ago by
Istvan Albert ♦♦ 78k
University Park, USA
Istvan Albert ♦♦ 78k 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 COMMENT • link written 5.3 years ago by Istvan Albert ♦♦ 78k

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

ADD REPLY • link written 5.3 years ago by joanne.lee • 0
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