Intersectbed Provides An Empty Output

Question

[joanne.lee]

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.

Answer 1

[Istvan Albert]

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

[joanne.lee]

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