Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: Intersectbed Provides An Empty Output
0
gravatar for joanne.lee
7.0 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 • 2.2k views
ADD COMMENT • link •
modified 7.0 years ago by Istvan Albert ♦♦ 84k • written 7.0 years ago by joanne.lee • 0
0
gravatar for Istvan Albert
7.0 years ago by
Istvan Albert ♦♦ 84k
University Park, USA
Istvan Albert ♦♦ 84k 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 7.0 years ago by Istvan Albert ♦♦ 84k

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 7.0 years ago by joanne.lee • 0
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1065 users visited in the last hour