Hello Dikla, Information in the sixth field of these same files will provide information about why the calculations for individual genes/transcripts were not performed. Possible values are explained in the tool documentation: http://cufflinks.cbcb.umd.edu/manual.html#gene_exp_diff This particular region appears to have low coverage compared to the surrounding regions (e.g. low abundance), but this is of course only a small sample, and it is difficult to know about other criteria considered by the tool from the graphic (proper pairing, multiple map locations, etc.). But if you believe that higher abundance transcripts are preventing lower abundance transcripts from being evaluated, or even just suspect that and want to test, you could try running Cufflinks with the option "Perform quartile normalization: Yes". Using "Perform Bias Correction: Yes" is also another parameter to explore (requires a reference genome). The Cufflinks web site is a great resource to learn more about these parameters and the Galaxy tool form has each included as an option. Hopefully this helps, Jen Galaxy team On 2/14/13 1:48 AM, Dikla Aharonovich wrote:
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
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