Running and Verifying bedtools

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Copy the test cases in the data directory to the TESTCASE directory.

   cd /path/to/BEDTOOLS/bedtools2/data
   cp gerp.chr1.bed.gz aluY.chr1.bed.gz /path/to/TESTCASE

3. Decompress the test case file.

   cd /path/to/TESTCASE
   gzip -d gerp.chr1.bed.gz
   gzip -d aluY.chr1.bed.gz

4. Generate the overlap of the two intersecting files.

   bedtools intersect -a aluY.chr1.bed -b gerp.chr1.bed

   If information similar to the following is displayed, the execution is successful.