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Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.

Cufflinks is available as a module on Apocrita.


To run the default installed version of Cufflinks, simply load the cufflinks module:

$ module load cufflinks
$ cufflinks

Usage:   cufflinks [options] <hits.sam>
General Options:
  -o/--output-dir              write all output files to this directory
  -p/--num-threads             number of threads used during analysis
  --seed                       value of random number generator seed
  -G/--GTF                     quantitate against reference transcript annotations
  -g/--GTF-guide               use reference transcript annotation to guide assembly
  -M/--mask-file               ignore all alignment within transcripts in this file
  -b/--frag-bias-correct       use bias correction - reference fasta required
  -u/--multi-read-correct      use 'rescue method' for multi-reads (more accurate)
  --library-type               library prep used for input reads
  --library-norm-method        Method used to normalize library sizes

For usage documentation, run cufflinks without any arguments.

Example job

Here is an example job using the Cufflinks test data, running on 1 core and 1GB of memory:

#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load cufflinks

cufflinks example.sam