It's not clear to me that reads per exon is a reasonable quantitation metric as many reads are likely to be split across two exons. That said, Cufflinks generates FPKMs by probabilistically assigning reads to transcripts based on both transcript and read characteristics (see http://cufflinks.cbcb.umd.edu/howitworks.html#hqua ), so I don't think there's a way to get Cufflinks to output FPKM by exon. You could try another RNA-seq quantitation package, such as RSEM: http://deweylab.biostat.wisc.edu/rsem/

On Apr 8, 2011, at 11:29 AM, Slim Sassi wrote:

Hello,
Is there a way to get FPKMs per exon? Maybe through modifying the GTF file to trick cufflinks into calculating FPKMs per exon instead of transcript or gene

Thanks

Slim

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