Cufflinks

Cufflinks [1] assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.

Running Cufflinks in HPC

Copy the job script "cufflinks.slurm" and input file "test_data.sam" from /usr/local/doc/CUFFLINKS to your home directory

cp /usr/local/doc/CUFFLINKS/* .

Run the job

sbatch cufflinks.slurm

You should see the following in your output file slurm.o<JobID>

...

[bam_header_read] EOF marker is absent. The input is probably truncated.

[bam_header_read] invalid BAM binary header (this is not a BAM file).

File ./test_data.sam doesn't appear to be a valid BAM file, trying SAM...

[16:03:56] Inspecting reads and determining fragment length distribution.

^M> Processed 1 loci. [*************************] 100%

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-len-std-dev) be provided.

> Map Properties:

> Normalized Map Mass: 102.50

> Raw Map Mass: 102.50

> Fragment Length Distribution: Truncated Gaussian (default)

> Default Mean: 200

> Default Std Dev: 80

[16:03:57] Assembling transcripts and estimating abundances.

... 100%

Also, check the other output files generated and copied back to your working directory.

References:

[1] Cufflinks GitHub