i will look later
there is a wellknown bug in cufflinks
i solved it once and it took me forever and will prob take me forever to remember...

On 14/02/2013 11:48, Dikla Aharonovich wrote:




We are using BAM to map Illumina reads to a bacterial genome, followed by Cufflinks o get the FPKMs.  We have come across many genes for which we get FPKM=0 (using both gene and transcript _expression_) even though there are reads mapping to these gene IDs (e.g. the region between the dashed lines in the attached screenshot).  Can anyone suggest a reason/fix for this?





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