Hello,

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?

Thanks

Dikla