Running and Verifying GMAP

Procedure

1. Use PuTTY to log in to the server as the root user.
2. View the GMAP version.

   gmap --verion

   If information similar to the following is displayed, GMAP has been installed:

   

3. Decompress the test case file.

   cd path/to/TESTCASE
   gzip -d human_g1k_v37.fasta.gz

4. Create a reference sequence index.

   mkdir human_index_home
   gmap_build -D /path/to/TESTCASE/human_index_home -d human_g1k_v37 human_g1k_v37.fasta

   

   • -D: index path.
   • -d: index file.
5. Perform the comparison.

   { time -p gmap -t 96 -D /path/to/TESTCASE/human_index_home -d human_g1k_v37 -f gff3_gene  human_g1k_v37.fasta; } 2>&1 |tee -a mapping_human.gff3

   

   -f: The output file is in gff3_gene format.

   If the mapping_human.gff3 file is generated, the execution is successful.