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  • cufflinks configuration

    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

  • #2
    that should work.
    /* Shawn Driscoll, Gene Expression Laboratory, Pfaff
    Salk Institute for Biological Studies, La Jolla, CA, USA */

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