FPKM/quantification problem for strand specific RNASeq

yosato

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Join Date: Nov 2015

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FPKM/quantification problem for strand specific RNASeq

11-09-2015, 06:57 PM

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
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