Running and Verifying Cufflinks
Procedure
- Use PuTTY to log in to the server as the root user.
- 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
- Run the following command to convert the test case format:
samtools view -bS accepted_hits.sam > accepted_hits.bam
- 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%
Parent topic: Cufflinks 2.2.1 Porting Guide (CentOS 7.6)