Running and Verifying Cufflinks

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following command to switch to the test file path of the source code and execute the file:

   cd /path/to/CUFFLINKS/cufflinks-master/external_tests/tiny_tests/2x75

3. Run the following command to convert the test case format:

   samtools view -bS accepted_hits.sam > accepted_hits.bam

4. Run the following command to run the test case:

   cufflinks accepted_hits.bam

   If the following information is displayed, the Cufflinks process ends properly:

   Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges.  It is recommended that correct parameters (--frag-len-mean and --frag-dev) be provided.
   > Map Properties:
   >       Normalized Map Mass: 90.00
   >       Raw Map Mass: 90.00
   >       Fragment Length Distribution: Truncated Gaussian (default)
   >                     Default Mean: 200
   >                  Default Std Dev: 80
   [19:58:21] Assembling transcripts and estimating abundances.
   > Processed 1 loci.                            [*************************] 100%