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  • yosato
    Junior Member
    • Nov 2015
    • 1
    #1

    FPKM/quantification problem for strand specific RNASeq

    Hi

    I am now analyzing strand-specific Illumina RNA-Seq data .

    #conditions are as follows
    *Sequencing Run(100bp paired-end , fr-secondstrand)
    *bam files were obtained by Tophat
    *FPKM values were estimated by cuffdiff/cufflinks with "--library-type fr-secondstrand" option

    FPKM values in genes.fpkm_tracking were completely same between with --library-type fr-secondstrand option and with --library-type fr-unstranded option.
    Strand aware mode seems not working in my analysis.

    Does anyone know why?
    Thank you in advance for your help

    Yosato
    Tags: None
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