Cufflinks¶
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.
Usage¶
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¶
Serial job¶
Here is an example job running on 1 core and 1GB of memory, using the Cufflinks test data.
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
module load cufflinks
cufflinks example.sam