cufflinks configuration

[mattia]

Hi,
I'm trying to define the best options configuration of Cufflinks. In order to estimate only known transcripts, is my command-line right or do I have to modify something?

cufflinks -u --compatible-hits-norm -b /human_hg19.fa -p 3 --library-type fr-secondstrand -G /transcripts.gtf -o output_dir /accepted_hits.bam

in which:
transcripts.gtf is the annotation file containing only known transcripts.

My data are generated from SOLiD 5500.

Thanks a lot,
Mattia

[sdriscoll]

that should work.