Cufflinks

module avail cufflinks/

Cufflinks 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.

Usage

Parallel run

Cuffdiff is not parallellized very well and bias correction is very slow for long transcripts, we recommend two stage processing using separate single-processor jobs for each sample

cuffquant -o S1_q -b ALL.fa merged.gtf S1/accepted_hits.bam

and then final (single-processor as well)

cuffdiff -o exp -b ALL.fa -L Cond1,Cond2 -u merged.gtf S1_q/abundances.cxb S2_q/abundances.cxb,S3_q/abundances.cxb